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 increased581778wt: 0.82 / mu: 0.91wt: AGTGCTGAGAATGAG
mu: AATGCTGAGAATGAG		 TGCT|gaga
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 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 0.76 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