Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 11 transcript(s)...
Querying Taster for transcript #1: ENST00000558014
Querying Taster for transcript #2: ENST00000536845
Querying Taster for transcript #3: ENST00000558816
Querying Taster for transcript #4: ENST00000316364
Querying Taster for transcript #5: ENST00000354744
Querying Taster for transcript #6: ENST00000358066
Querying Taster for transcript #7: ENST00000389428
Querying Taster for transcript #8: ENST00000537942
Querying Taster for transcript #9: ENST00000389433
Querying Taster for transcript #10: ENST00000389432
Querying Taster for transcript #11: ENST00000355997
MT speed 0 s - this script 6.874276 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file
SEMA6Dpolymorphism_automatic1simple_aaeaffectedS478Nsingle base exchangers532598show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000558014
Genbank transcript ID NM_001198999
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1989G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3036 / 3036
position (AA) of stopcodon in wt / mu AA sequence 1012 / 1012
position of stopcodon in wt / mu cDNA 3592 / 3592
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 557 / 557
chromosome 15
strand 1
last intron/exon boundary 2304
theoretical NMD boundary in CDS 1697
length of CDS 3036
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1989
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHGVRWEVQS GESNQMVHMN
VLITCVFAAF VLGAFIAGVA VYCYRDMFVR KNRKIHKDAE SAQSCTDSSG SFAKLNGLFD
SPVKEYQQNI DSPKLYSNLL TSRKELPPNG DTKSMVMDHR GQPPELAALP TPESTPVLHQ
KTLQAMKSHS EKAHGHGASR KETPQFFPSS PPPHSPLSHG HIPSAIVLPN ATHDYNTSFS
NSNAHKAEKK LQNIDHPLTK SSSKRDHRRS VDSRNTLNDL LKHLNDPNSN PKAIMGDIQM
AHQNLMLDPM GSMSEVPPKV PNREASLYSP PSTLPRNSPT KRVDVPTTPG VPMTSLERQR
GYHKNSSQRH SISAMPKNLN SPNGVLLSRQ PSMNRGGYMP TPTGAKVDYI QGTPVSVHLQ
PSLSRQSSYT SNGTLPRTGL KRTPSLKPDV PPKPSFVPQT PSVRPLNKYT Y*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHGVRWEVQS GESNQMVHMN
VLITCVFAAF VLGAFIAGVA VYCYRDMFVR KNRKIHKDAE SAQSCTDSSG SFAKLNGLFD
SPVKEYQQNI DSPKLYSNLL TSRKELPPNG DTKSMVMDHR GQPPELAALP TPESTPVLHQ
KTLQAMKSHS EKAHGHGASR KETPQFFPSS PPPHSPLSHG HIPSAIVLPN ATHDYNTSFS
NSNAHKAEKK LQNIDHPLTK SSSKRDHRRS VDSRNTLNDL LKHLNDPNSN PKAIMGDIQM
AHQNLMLDPM GSMSEVPPKV PNREASLYSP PSTLPRNSPT KRVDVPTTPG VPMTSLERQR
GYHKNSSQRH SISAMPKNLN SPNGVLLSRQ PSMNRGGYMP TPTGAKVDYI QGTPVSVHLQ
PSLSRQSSYT SNGTLPRTGL KRTPSLKPDV PPKPSFVPQT PSVRPLNKYT Y*
speed 0.63 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000558816
Genbank transcript ID N/A
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1723G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1794 / 1794
position (AA) of stopcodon in wt / mu AA sequence 598 / 598
position of stopcodon in wt / mu cDNA 2084 / 2084
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 291 / 291
chromosome 15
strand 1
last intron/exon boundary 2034
theoretical NMD boundary in CDS 1693
length of CDS 1794
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1723
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHD MEVSSSSVTT MVYDGKSSLE SPTRWST*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHD MEVSSSSVTT MVYDGKSSLE SPTRWST*
speed 0.59 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000536845
Genbank transcript ID N/A
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1817G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3222 / 3222
position (AA) of stopcodon in wt / mu AA sequence 1074 / 1074
position of stopcodon in wt / mu cDNA 3606 / 3606
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 385 / 385
chromosome 15
strand 1
last intron/exon boundary 2318
theoretical NMD boundary in CDS 1883
length of CDS 3222
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1817
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSDM EVSSSSVTTM
ASIPEITPKV IDTWRPKLTS SRKFVVQDDP NTSDFTDPLS GIPKGVRWEV QSGESNQMVH
MNVLITCVFA AFVLGAFIAG VAVYCYRDMF VRKNRKIHKD AESAQSCTDS SGSFAKLNGL
FDSPVKEYQQ NIDSPKLYSN LLTSRKELPP NGDTKSMVMD HRGQPPELAA LPTPESTPVL
HQKTLQAMKS HSEKAHGHGA SRKETPQFFP SSPPPHSPLS HGHIPSAIVL PNATHDYNTS
FSNSNAHKAE KKLQNIDHPL TKSSSKRDHR RSVDSRNTLN DLLKHLNDPN SNPKAIMGDI
QMAHQNLMLD PMGSMSEVPP KVPNREASLY SPPSTLPRNS PTKRVDVPTT PGVPMTSLER
QRGYHKNSSQ RHSISAMPKN LNSPNGVLLS RQPSMNRGGY MPTPTGAKVD YIQGTPVSVH
LQPSLSRQSS YTSNGTLPRT GLKRTPSLKP DVPPKPSFVP QTPSVRPLNK YTY*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSDM EVSSSSVTTM
ASIPEITPKV IDTWRPKLTS SRKFVVQDDP NTSDFTDPLS GIPKGVRWEV QSGESNQMVH
MNVLITCVFA AFVLGAFIAG VAVYCYRDMF VRKNRKIHKD AESAQSCTDS SGSFAKLNGL
FDSPVKEYQQ NIDSPKLYSN LLTSRKELPP NGDTKSMVMD HRGQPPELAA LPTPESTPVL
HQKTLQAMKS HSEKAHGHGA SRKETPQFFP SSPPPHSPLS HGHIPSAIVL PNATHDYNTS
FSNSNAHKAE KKLQNIDHPL TKSSSKRDHR RSVDSRNTLN DLLKHLNDPN SNPKAIMGDI
QMAHQNLMLD PMGSMSEVPP KVPNREASLY SPPSTLPRNS PTKRVDVPTT PGVPMTSLER
QRGYHKNSSQ RHSISAMPKN LNSPNGVLLS RQPSMNRGGY MPTPTGAKVD YIQGTPVSVH
LQPSLSRQSS YTSNGTLPRT GLKRTPSLKP DVPPKPSFVP QTPSVRPLNK YTY*
speed 0.63 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000316364
Genbank transcript ID NM_153618
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1872G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3222 / 3222
position (AA) of stopcodon in wt / mu AA sequence 1074 / 1074
position of stopcodon in wt / mu cDNA 3661 / 3661
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 440 / 440
chromosome 15
strand 1
last intron/exon boundary 2373
theoretical NMD boundary in CDS 1883
length of CDS 3222
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1872
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSDM EVSSSSVTTM
ASIPEITPKV IDTWRPKLTS SRKFVVQDDP NTSDFTDPLS GIPKGVRWEV QSGESNQMVH
MNVLITCVFA AFVLGAFIAG VAVYCYRDMF VRKNRKIHKD AESAQSCTDS SGSFAKLNGL
FDSPVKEYQQ NIDSPKLYSN LLTSRKELPP NGDTKSMVMD HRGQPPELAA LPTPESTPVL
HQKTLQAMKS HSEKAHGHGA SRKETPQFFP SSPPPHSPLS HGHIPSAIVL PNATHDYNTS
FSNSNAHKAE KKLQNIDHPL TKSSSKRDHR RSVDSRNTLN DLLKHLNDPN SNPKAIMGDI
QMAHQNLMLD PMGSMSEVPP KVPNREASLY SPPSTLPRNS PTKRVDVPTT PGVPMTSLER
QRGYHKNSSQ RHSISAMPKN LNSPNGVLLS RQPSMNRGGY MPTPTGAKVD YIQGTPVSVH
LQPSLSRQSS YTSNGTLPRT GLKRTPSLKP DVPPKPSFVP QTPSVRPLNK YTY*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSDM EVSSSSVTTM
ASIPEITPKV IDTWRPKLTS SRKFVVQDDP NTSDFTDPLS GIPKGVRWEV QSGESNQMVH
MNVLITCVFA AFVLGAFIAG VAVYCYRDMF VRKNRKIHKD AESAQSCTDS SGSFAKLNGL
FDSPVKEYQQ NIDSPKLYSN LLTSRKELPP NGDTKSMVMD HRGQPPELAA LPTPESTPVL
HQKTLQAMKS HSEKAHGHGA SRKETPQFFP SSPPPHSPLS HGHIPSAIVL PNATHDYNTS
FSNSNAHKAE KKLQNIDHPL TKSSSKRDHR RSVDSRNTLN DLLKHLNDPN SNPKAIMGDI
QMAHQNLMLD PMGSMSEVPP KVPNREASLY SPPSTLPRNS PTKRVDVPTT PGVPMTSLER
QRGYHKNSSQ RHSISAMPKN LNSPNGVLLS RQPSMNRGGY MPTPTGAKVD YIQGTPVSVH
LQPSLSRQSS YTSNGTLPRT GLKRTPSLKP DVPPKPSFVP QTPSVRPLNK YTY*
speed 0.44 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000354744
Genbank transcript ID NM_153617
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1872G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3054 / 3054
position (AA) of stopcodon in wt / mu AA sequence 1018 / 1018
position of stopcodon in wt / mu cDNA 3493 / 3493
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 440 / 440
chromosome 15
strand 1
last intron/exon boundary 2205
theoretical NMD boundary in CDS 1715
length of CDS 3054
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1872
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSGV RWEVQSGESN
QMVHMNVLIT CVFAAFVLGA FIAGVAVYCY RDMFVRKNRK IHKDAESAQS CTDSSGSFAK
LNGLFDSPVK EYQQNIDSPK LYSNLLTSRK ELPPNGDTKS MVMDHRGQPP ELAALPTPES
TPVLHQKTLQ AMKSHSEKAH GHGASRKETP QFFPSSPPPH SPLSHGHIPS AIVLPNATHD
YNTSFSNSNA HKAEKKLQNI DHPLTKSSSK RDHRRSVDSR NTLNDLLKHL NDPNSNPKAI
MGDIQMAHQN LMLDPMGSMS EVPPKVPNRE ASLYSPPSTL PRNSPTKRVD VPTTPGVPMT
SLERQRGYHK NSSQRHSISA MPKNLNSPNG VLLSRQPSMN RGGYMPTPTG AKVDYIQGTP
VSVHLQPSLS RQSSYTSNGT LPRTGLKRTP SLKPDVPPKP SFVPQTPSVR PLNKYTY*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSGV RWEVQSGESN
QMVHMNVLIT CVFAAFVLGA FIAGVAVYCY RDMFVRKNRK IHKDAESAQS CTDSSGSFAK
LNGLFDSPVK EYQQNIDSPK LYSNLLTSRK ELPPNGDTKS MVMDHRGQPP ELAALPTPES
TPVLHQKTLQ AMKSHSEKAH GHGASRKETP QFFPSSPPPH SPLSHGHIPS AIVLPNATHD
YNTSFSNSNA HKAEKKLQNI DHPLTKSSSK RDHRRSVDSR NTLNDLLKHL NDPNSNPKAI
MGDIQMAHQN LMLDPMGSMS EVPPKVPNRE ASLYSPPSTL PRNSPTKRVD VPTTPGVPMT
SLERQRGYHK NSSQRHSISA MPKNLNSPNG VLLSRQPSMN RGGYMPTPTG AKVDYIQGTP
VSVHLQPSLS RQSSYTSNGT LPRTGLKRTP SLKPDVPPKP SFVPQTPSVR PLNKYTY*
speed 0.87 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000358066
Genbank transcript ID NM_020858
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1872G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3036 / 3036
position (AA) of stopcodon in wt / mu AA sequence 1012 / 1012
position of stopcodon in wt / mu cDNA 3475 / 3475
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 440 / 440
chromosome 15
strand 1
last intron/exon boundary 2187
theoretical NMD boundary in CDS 1697
length of CDS 3036
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1872
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHGVRWEVQS GESNQMVHMN
VLITCVFAAF VLGAFIAGVA VYCYRDMFVR KNRKIHKDAE SAQSCTDSSG SFAKLNGLFD
SPVKEYQQNI DSPKLYSNLL TSRKELPPNG DTKSMVMDHR GQPPELAALP TPESTPVLHQ
KTLQAMKSHS EKAHGHGASR KETPQFFPSS PPPHSPLSHG HIPSAIVLPN ATHDYNTSFS
NSNAHKAEKK LQNIDHPLTK SSSKRDHRRS VDSRNTLNDL LKHLNDPNSN PKAIMGDIQM
AHQNLMLDPM GSMSEVPPKV PNREASLYSP PSTLPRNSPT KRVDVPTTPG VPMTSLERQR
GYHKNSSQRH SISAMPKNLN SPNGVLLSRQ PSMNRGGYMP TPTGAKVDYI QGTPVSVHLQ
PSLSRQSSYT SNGTLPRTGL KRTPSLKPDV PPKPSFVPQT PSVRPLNKYT Y*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHGVRWEVQS GESNQMVHMN
VLITCVFAAF VLGAFIAGVA VYCYRDMFVR KNRKIHKDAE SAQSCTDSSG SFAKLNGLFD
SPVKEYQQNI DSPKLYSNLL TSRKELPPNG DTKSMVMDHR GQPPELAALP TPESTPVLHQ
KTLQAMKSHS EKAHGHGASR KETPQFFPSS PPPHSPLSHG HIPSAIVLPN ATHDYNTSFS
NSNAHKAEKK LQNIDHPLTK SSSKRDHRRS VDSRNTLNDL LKHLNDPNSN PKAIMGDIQM
AHQNLMLDPM GSMSEVPPKV PNREASLYSP PSTLPRNSPT KRVDVPTTPG VPMTSLERQR
GYHKNSSQRH SISAMPKNLN SPNGVLLSRQ PSMNRGGYMP TPTGAKVDYI QGTPVSVHLQ
PSLSRQSSYT SNGTLPRTGL KRTPSLKPDV PPKPSFVPQT PSVRPLNKYT Y*
speed 0.99 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000389428
Genbank transcript ID NM_153616
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1872G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2997 / 2997
position (AA) of stopcodon in wt / mu AA sequence 999 / 999
position of stopcodon in wt / mu cDNA 3436 / 3436
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 440 / 440
chromosome 15
strand 1
last intron/exon boundary 2148
theoretical NMD boundary in CDS 1658
length of CDS 2997
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1872
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHG VRWEVQSGES NQMVHMNVLI TCVFAAFVLG
AFIAGVAVYC YRDMFVRKNR KIHKDAESAQ SCTDSSGSFA KLNGLFDSPV KEYQQNIDSP
KLYSNLLTSR KELPPNGDTK SMVMDHRGQP PELAALPTPE STPVLHQKTL QAMKSHSEKA
HGHGASRKET PQFFPSSPPP HSPLSHGHIP SAIVLPNATH DYNTSFSNSN AHKAEKKLQN
IDHPLTKSSS KRDHRRSVDS RNTLNDLLKH LNDPNSNPKA IMGDIQMAHQ NLMLDPMGSM
SEVPPKVPNR EASLYSPPST LPRNSPTKRV DVPTTPGVPM TSLERQRGYH KNSSQRHSIS
AMPKNLNSPN GVLLSRQPSM NRGGYMPTPT GAKVDYIQGT PVSVHLQPSL SRQSSYTSNG
TLPRTGLKRT PSLKPDVPPK PSFVPQTPSV RPLNKYTY*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHG VRWEVQSGES NQMVHMNVLI TCVFAAFVLG
AFIAGVAVYC YRDMFVRKNR KIHKDAESAQ SCTDSSGSFA KLNGLFDSPV KEYQQNIDSP
KLYSNLLTSR KELPPNGDTK SMVMDHRGQP PELAALPTPE STPVLHQKTL QAMKSHSEKA
HGHGASRKET PQFFPSSPPP HSPLSHGHIP SAIVLPNATH DYNTSFSNSN AHKAEKKLQN
IDHPLTKSSS KRDHRRSVDS RNTLNDLLKH LNDPNSNPKA IMGDIQMAHQ NLMLDPMGSM
SEVPPKVPNR EASLYSPPST LPRNSPTKRV DVPTTPGVPM TSLERQRGYH KNSSQRHSIS
AMPKNLNSPN GVLLSRQPSM NRGGYMPTPT GAKVDYIQGT PVSVHLQPSL SRQSSYTSNG
TLPRTGLKRT PSLKPDVPPK PSFVPQTPSV RPLNKYTY*
speed 0.87 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000355997
Genbank transcript ID NM_153619
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1872G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1794 / 1794
position (AA) of stopcodon in wt / mu AA sequence 598 / 598
position of stopcodon in wt / mu cDNA 2233 / 2233
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 440 / 440
chromosome 15
strand 1
last intron/exon boundary 2183
theoretical NMD boundary in CDS 1693
length of CDS 1794
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1872
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHD MEVSSSSVTT MVYDGKSSLE SPTRWST*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHD MEVSSSSVTT MVYDGKSSLE SPTRWST*
speed 0.86 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000537942
Genbank transcript ID N/A
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1674G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3036 / 3036
position (AA) of stopcodon in wt / mu AA sequence 1012 / 1012
position of stopcodon in wt / mu cDNA 3277 / 3277
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 242 / 242
chromosome 15
strand 1
last intron/exon boundary 1989
theoretical NMD boundary in CDS 1697
length of CDS 3036
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1674
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHGVRWEVQS GESNQMVHMN
VLITCVFAAF VLGAFIAGVA VYCYRDMFVR KNRKIHKDAE SAQSCTDSSG SFAKLNGLFD
SPVKEYQQNI DSPKLYSNLL TSRKELPPNG DTKSMVMDHR GQPPELAALP TPESTPVLHQ
KTLQAMKSHS EKAHGHGASR KETPQFFPSS PPPHSPLSHG HIPSAIVLPN ATHDYNTSFS
NSNAHKAEKK LQNIDHPLTK SSSKRDHRRS VDSRNTLNDL LKHLNDPNSN PKAIMGDIQM
AHQNLMLDPM GSMSEVPPKV PNREASLYSP PSTLPRNSPT KRVDVPTTPG VPMTSLERQR
GYHKNSSQRH SISAMPKNLN SPNGVLLSRQ PSMNRGGYMP TPTGAKVDYI QGTPVSVHLQ
PSLSRQSSYT SNGTLPRTGL KRTPSLKPDV PPKPSFVPQT PSVRPLNKYT Y*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHGVRWEVQS GESNQMVHMN
VLITCVFAAF VLGAFIAGVA VYCYRDMFVR KNRKIHKDAE SAQSCTDSSG SFAKLNGLFD
SPVKEYQQNI DSPKLYSNLL TSRKELPPNG DTKSMVMDHR GQPPELAALP TPESTPVLHQ
KTLQAMKSHS EKAHGHGASR KETPQFFPSS PPPHSPLSHG HIPSAIVLPN ATHDYNTSFS
NSNAHKAEKK LQNIDHPLTK SSSKRDHRRS VDSRNTLNDL LKHLNDPNSN PKAIMGDIQM
AHQNLMLDPM GSMSEVPPKV PNREASLYSP PSTLPRNSPT KRVDVPTTPG VPMTSLERQR
GYHKNSSQRH SISAMPKNLN SPNGVLLSRQ PSMNRGGYMP TPTGAKVDYI QGTPVSVHLQ
PSLSRQSSYT SNGTLPRTGL KRTPSLKPDV PPKPSFVPQT PSVRPLNKYT Y*
speed 0.62 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000389433
Genbank transcript ID N/A
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1872G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3165 / 3165
position (AA) of stopcodon in wt / mu AA sequence 1055 / 1055
position of stopcodon in wt / mu cDNA 3604 / 3604
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 440 / 440
chromosome 15
strand 1
last intron/exon boundary 2316
theoretical NMD boundary in CDS 1826
length of CDS 3165
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1872
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHD MEVSSSSVTT MASIPEITPK VIDTWRPKLT
SSRKFVVQDD PNTSDFTDPL SGIPKGVRWE VQSGESNQMV HMNVLITCVF AAFVLGAFIA
GVAVYCYRDM FVRKNRKIHK DAESAQSCTD SSGSFAKLNG LFDSPVKEYQ QNIDSPKLYS
NLLTSRKELP PNGDTKSMVM DHRGQPPELA ALPTPESTPV LHQKTLQAMK SHSEKAHGHG
ASRKETPQFF PSSPPPHSPL SHGHIPSAIV LPNATHDYNT SFSNSNAHKA EKKLQNIDHP
LTKSSSKRDH RRSVDSRNTL NDLLKHLNDP NSNPKAIMGD IQMAHQNLML DPMGSMSEVP
PKVPNREASL YSPPSTLPRN SPTKRVDVPT TPGVPMTSLE RQRGYHKNSS QRHSISAMPK
NLNSPNGVLL SRQPSMNRGG YMPTPTGAKV DYIQGTPVSV HLQPSLSRQS SYTSNGTLPR
TGLKRTPSLK PDVPPKPSFV PQTPSVRPLN KYTY*
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHD MEVSSSSVTT MASIPEITPK VIDTWRPKLT
SSRKFVVQDD PNTSDFTDPL SGIPKGVRWE VQSGESNQMV HMNVLITCVF AAFVLGAFIA
GVAVYCYRDM FVRKNRKIHK DAESAQSCTD SSGSFAKLNG LFDSPVKEYQ QNIDSPKLYS
NLLTSRKELP PNGDTKSMVM DHRGQPPELA ALPTPESTPV LHQKTLQAMK SHSEKAHGHG
ASRKETPQFF PSSPPPHSPL SHGHIPSAIV LPNATHDYNT SFSNSNAHKA EKKLQNIDHP
LTKSSSKRDH RRSVDSRNTL NDLLKHLNDP NSNPKAIMGD IQMAHQNLML DPMGSMSEVP
PKVPNREASL YSPPSTLPRN SPTKRVDVPT TPGVPMTSLE RQRGYHKNSS QRHSISAMPK
NLNSPNGVLL SRQPSMNRGG YMPTPTGAKV DYIQGTPVSV HLQPSLSRQS SYTSNGTLPR
TGLKRTPSLK PDVPPKPSFV PQTPSVRPLN KYTY*
speed 0.61 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.59737724810123e-134 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:48058071G>AN/A show variant in all transcripts   IGV
HGNC symbol SEMA6D
Ensembl transcript ID ENST00000389432
Genbank transcript ID N/A
UniProt peptide Q8NFY4
alteration type single base exchange
alteration region CDS
DNA changes c.1433G>A
cDNA.1872G>A
g.581774G>A
AA changes S478N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 478
frameshift no
known variant Reference ID: rs532598
databasehomozygous (A/A)heterozygousallele carriers
1000G56312061769
ExAC91761441523591
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9070.493
0.0660.36
(flanking)-0.0010.359
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor decreased581768wt: 0.95 / mu: 0.27wt: AAATAGGTGCAGTGC
mu: AAATAGGTGCAATGC		 ATAG|gtgc
Donor marginally increased581775wt: 0.9602 / mu: 0.9895 (marginal change - not scored)wt: TGCAGTGCTGAGAAT
mu: TGCAATGCTGAGAAT		 CAGT|gctg
Donor increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
Donor gained5817700.88mu: ATAGGTGCAATGCTG AGGT|gcaa
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      478EEIEAYNHAKCSAENEEDKKVISL
mutated  all conserved    478EEIEAYNHAKCNAE
Ptroglodytes  all identical  ENSPTRG00000007040  478EEIEAYNHAKCSAE
Mmulatta  all identical  ENSMMUG00000012144  480EEIEAYNHAKCSAENEEDKKVIS
Fcatus  all conserved  ENSFCAG00000010985  478EEIEAYNHAKCNAE
Mmusculus  all identical  ENSMUSG00000027200  478EEIEAYNPAKCSAE
Ggallus  all conserved  ENSGALG00000004844  481NAESEEDRRVIS
Trubripes  not conserved  ENSTRUG00000016974  480EEIDVFNRAKCLSNREDDKRVLS
Drerio  not conserved  ENSDARG00000011533  481EEIDVFNQAKCLSSNEDDRRIL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000018391  478EEIDAYNRAKCSGNSEEDRK
protein features
start (aa)end (aa)featuredetails 
21662TOPO_DOMExtracellular (Potential).lost
27512DOMAINSema.lost
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
506506DISULFIDBy similarity.might get lost (downstream of altered splice site)
514569DOMAINPSI.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
521521DISULFIDBy similarity.might get lost (downstream of altered splice site)
525525DISULFIDBy similarity.might get lost (downstream of altered splice site)
533533DISULFIDBy similarity.might get lost (downstream of altered splice site)
541541DISULFIDBy similarity.might get lost (downstream of altered splice site)
568568DISULFIDBy similarity.might get lost (downstream of altered splice site)
631631CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
663683TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6841073TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3093 / 3093
position (AA) of stopcodon in wt / mu AA sequence 1031 / 1031
position of stopcodon in wt / mu cDNA 3532 / 3532
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 440 / 440
chromosome 15
strand 1
last intron/exon boundary 2244
theoretical NMD boundary in CDS 1754
length of CDS 3093
coding sequence (CDS) position 1433
cDNA position
(for ins/del: last normal base / first normal base)		 1872
gDNA position
(for ins/del: last normal base / first normal base)		 581774
chromosomal position
(for ins/del: last normal base / first normal base)		 48058071
original gDNA sequence snippet TATCCCACAAAATAGGTGCAGTGCTGAGAATGAGGAAGACA
altered gDNA sequence snippet TATCCCACAAAATAGGTGCAATGCTGAGAATGAGGAAGACA
original cDNA sequence snippet CTACAACCATGCAAAGTGCAGTGCTGAGAATGAGGAAGACA
altered cDNA sequence snippet CTACAACCATGCAAAGTGCAATGCTGAGAATGAGGAAGACA
wildtype AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHEILPTSTT PDYKIFGGPT
SGVRWEVQSG ESNQMVHMNV LITCVFAAFV LGAFIAGVAV YCYRDMFVRK NRKIHKDAES
AQSCTDSSGS FAKLNGLFDS PVKEYQQNID SPKLYSNLLT SRKELPPNGD TKSMVMDHRG
QPPELAALPT PESTPVLHQK TLQAMKSHSE KAHGHGASRK ETPQFFPSSP PPHSPLSHGH
IPSAIVLPNA THDYNTSFSN SNAHKAEKKL QNIDHPLTKS SSKRDHRRSV DSRNTLNDLL
KHLNDPNSNP KAIMGDIQMA HQNLMLDPMG SMSEVPPKVP NREASLYSPP STLPRNSPTK
RVDVPTTPGV PMTSLERQRG YHKNSSQRHS ISAMPKNLNS PNGVLLSRQP SMNRGGYMPT
PTGAKVDYIQ GTPVSVHLQP SLSRQSSYTS NGTLPRTGLK RTPSLKPDVP PKPSFVPQTP
SVRPLNKYTY *
mutated AA sequence MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCNAE
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS
CGRVTPGMLL LTEDFFAFHN HSAEGYEQDT EFGNTAHLGD CHEILPTSTT PDYKIFGGPT
SGVRWEVQSG ESNQMVHMNV LITCVFAAFV LGAFIAGVAV YCYRDMFVRK NRKIHKDAES
AQSCTDSSGS FAKLNGLFDS PVKEYQQNID SPKLYSNLLT SRKELPPNGD TKSMVMDHRG
QPPELAALPT PESTPVLHQK TLQAMKSHSE KAHGHGASRK ETPQFFPSSP PPHSPLSHGH
IPSAIVLPNA THDYNTSFSN SNAHKAEKKL QNIDHPLTKS SSKRDHRRSV DSRNTLNDLL
KHLNDPNSNP KAIMGDIQMA HQNLMLDPMG SMSEVPPKVP NREASLYSPP STLPRNSPTK
RVDVPTTPGV PMTSLERQRG YHKNSSQRHS ISAMPKNLNS PNGVLLSRQP SMNRGGYMPT
PTGAKVDYIQ GTPVSVHLQP SLSRQSSYTS NGTLPRTGLK RTPSLKPDVP PKPSFVPQTP
SVRPLNKYTY *
speed 0.90 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Problems