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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000287097
Querying Taster for transcript #2: ENST00000437994
Querying Taster for transcript #3: ENST00000422508
MT speed 0 s - this script 2.650866 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CD109polymorphism_automatic3.43703894779557e-05simple_aaeaffectedY703Ssingle base exchangers10455097show file
CD109polymorphism_automatic3.43703894779557e-05simple_aaeaffectedY703Ssingle base exchangers10455097show file
CD109polymorphism_automatic4.47526520810371e-05simple_aaeaffectedY626Ssingle base exchangers10455097show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999965629610522 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM020385)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:74493432A>CN/A show variant in all transcripts   IGV
HGNC symbol CD109
Ensembl transcript ID ENST00000287097
Genbank transcript ID NM_133493
UniProt peptide Q6YHK3
alteration type single base exchange
alteration region CDS
DNA changes c.2108A>C
cDNA.2220A>C
g.87925A>C
AA changes Y703S Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 703
frameshift no
known variant Reference ID: rs10455097
databasehomozygous (C/C)heterozygousallele carriers
1000G71011621872
ExAC1599777316770

known disease mutation at this position, please check HGMD for details (HGMD ID CM020385)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.630.98
1.4660.883
(flanking)-0.4970.003
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost87922sequence motif lost- wt: tcag|TTAC
 mu: tcag.TTCC
Acc marginally increased87920wt: 0.3423 / mu: 0.3566 (marginal change - not scored)wt: TATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAGA
mu: TATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAGA		 cttc|AGTT
Acc marginally increased87921wt: 0.9590 / mu: 0.9605 (marginal change - not scored)wt: ATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAGAA
mu: ATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAGAA		 ttca|GTTA
Acc increased87919wt: 0.28 / mu: 0.35wt: TTATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAG
mu: TTATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAG		 actt|CAGT
Acc marginally increased87916wt: 0.8542 / mu: 0.8766 (marginal change - not scored)wt: TGTTTATATTTATTATCTTGACTTCAGTTACAGGATTTACC
mu: TGTTTATATTTATTATCTTGACTTCAGTTCCAGGATTTACC		 ttga|CTTC
Donor increased87916wt: 0.42 / mu: 0.62wt: TCTTGACTTCAGTTA
mu: TCTTGACTTCAGTTC		 TTGA|cttc
Acc gained879270.75mu: ATTATCTTGACTTCAGTTCCAGGATTTACCAAGAATTTGAA tcca|GGAT
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      703ETWIWLDTNMGYRIYQEFEVTVPD
mutated  not conserved    703ETWIWLDTNMGSRIYQEFEVTVP
Ptroglodytes  not conserved  ENSPTRG00000018349  703ETWIWLDTNMGSRIYQEFEVTVP
Mmulatta  not conserved  ENSMMUG00000017806  703ETWIWLDTNMGSRIYQEFEVTVP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000046186  705ETWIWLDAYMGSKIYEEFEVT
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060609  738ETWIWLDANVSDSASAVFSLTVP
Dmelanogaster  no homologue    
Celegans  not conserved  ZK337.1  755HTWIWSDLNSTSGEV-EMEIEA
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
593702REGIONBait region (approximate) (By similarity).might get lost (downstream of altered splice site)
789789CONFLICTK -> E (in Ref. 4; BAG36395).might get lost (downstream of altered splice site)
803803CONFLICTG -> S (in Ref. 2; AAN78483).might get lost (downstream of altered splice site)
921924CROSSLNKIsoglutamyl cysteine thioester (Cys-Gln) (By similarity).might get lost (downstream of altered splice site)
10461046CONFLICTV -> A (in Ref. 5; ABQ66266).might get lost (downstream of altered splice site)
10861086CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14181418CONFLICTD -> N (in Ref. 4; BAG53987).might get lost (downstream of altered splice site)
14201420LIPIDGPI-anchor amidated alanine (Potential).might get lost (downstream of altered splice site)
14211445PROPEPRemoved in mature form (Potential). /FTId=PRO_0000255946.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4338 / 4338
position (AA) of stopcodon in wt / mu AA sequence 1446 / 1446
position of stopcodon in wt / mu cDNA 4450 / 4450
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 113 / 113
chromosome 6
strand 1
last intron/exon boundary 4275
theoretical NMD boundary in CDS 4112
length of CDS 4338
coding sequence (CDS) position 2108
cDNA position
(for ins/del: last normal base / first normal base)		 2220
gDNA position
(for ins/del: last normal base / first normal base)		 87925
chromosomal position
(for ins/del: last normal base / first normal base)		 74493432
original gDNA sequence snippet TTATTATCTTGACTTCAGTTACAGGATTTACCAAGAATTTG
altered gDNA sequence snippet TTATTATCTTGACTTCAGTTCCAGGATTTACCAAGAATTTG
original cDNA sequence snippet GCTAGACACCAACATGGGTTACAGGATTTACCAAGAATTTG
altered cDNA sequence snippet GCTAGACACCAACATGGGTTCCAGGATTTACCAAGAATTTG
wildtype AA sequence MQGPPLLTAA HLLCVCTAAL AVAPGPRFLV TAPGIIRPGG NVTIGVELLE HCPSQVTVKA
ELLKTASNLT VSVLEAEGVF EKGSFKTLTL PSLPLNSADE IYELRVTGRT QDEILFSNST
RLSFETKRIS VFIQTDKALY KPKQEVKFRI VTLFSDFKPY KTSLNILIKD PKSNLIQQWL
SQQSDLGVIS KTFQLSSHPI LGDWSIQVQV NDQTYYQSFQ VSEYVLPKFE VTLQTPLYCS
MNSKHLNGTI TAKYTYGKPV KGDVTLTFLP LSFWGKKKNI TKTFKINGSA NFSFNDEEMK
NVMDSSNGLS EYLDLSSPGP VEILTTVTES VTGISRNVST NVFFKQHDYI IEFFDYTTVL
KPSLNFTATV KVTRADGNQL TLEERRNNVV ITVTQRNYTE YWSGSNSGNQ KMEAVQKINY
TVPQSGTFKI EFPILEDSSE LQLKAYFLGS KSSMAVHSLF KSPSKTYIQL KTRDENIKVG
SPFELVVSGN KRLKELSYMV VSRGQLVAVG KQNSTMFSLT PENSWTPKAC VIVYYIEDDG
EIISDVLKIP VQLVFKNKIK LYWSKVKAEP SEKVSLRISV TQPDSIVGIV AVDKSVNLMN
ASNDITMENV VHELELYNTG YYLGMFMNSF AVFQECGLWV LTDANLTKDY IDGVYDNAEY
AERFMEENEG HIVDIHDFSL GSSPHVRKHF PETWIWLDTN MGYRIYQEFE VTVPDSITSW
VATGFVISED LGLGLTTTPV ELQAFQPFFI FLNLPYSVIR GEEFALEITI FNYLKDATEV
KVIIEKSDKF DILMTSNEIN ATGHQQTLLV PSEDGATVLF PIRPTHLGEI PITVTALSPT
ASDAVTQMIL VKAEGIEKSY SQSILLDLTD NRLQSTLKTL SFSFPPNTVT GSERVQITAI
GDVLGPSING LASLIRMPYG CGEQNMINFA PNIYILDYLT KKKQLTDNLK EKALSFMRQG
YQRELLYQRE DGSFSAFGNY DPSGSTWLSA FVLRCFLEAD PYIDIDQNVL HRTYTWLKGH
QKSNGEFWDP GRVIHSELQG GNKSPVTLTA YIVTSLLGYR KYQPNIDVQE SIHFLESEFS
RGISDNYTLA LITYALSSVG SPKAKEALNM LTWRAEQEGG MQFWVSSESK LSDSWQPRSL
DIEVAAYALL SHFLQFQTSE GIPIMRWLSR QRNSLGGFAS TQDTTVALKA LSEFAALMNT
ERTNIQVTVT GPSSPSPVKF LIDTHNRLLL QTAELAVVQP TAVNISANGF GFAICQLNVV
YNVKASGSSR RRRSIQNQEA FDLDVAVKEN KDDLNHVDLN VCTSFSGPGR SGMALMEVNL
LSGFMVPSEA ISLSETVKKV EYDHGKLNLY LDSVNETQFC VNIPAVRNFK VSNTQDASVS
IVDYYEPRRQ AVRSYNSEVK LSSCDLCSDV QGCRPCEDGA SGSHHHSSVI FIFCFKLLYF
MELWL*
mutated AA sequence MQGPPLLTAA HLLCVCTAAL AVAPGPRFLV TAPGIIRPGG NVTIGVELLE HCPSQVTVKA
ELLKTASNLT VSVLEAEGVF EKGSFKTLTL PSLPLNSADE IYELRVTGRT QDEILFSNST
RLSFETKRIS VFIQTDKALY KPKQEVKFRI VTLFSDFKPY KTSLNILIKD PKSNLIQQWL
SQQSDLGVIS KTFQLSSHPI LGDWSIQVQV NDQTYYQSFQ VSEYVLPKFE VTLQTPLYCS
MNSKHLNGTI TAKYTYGKPV KGDVTLTFLP LSFWGKKKNI TKTFKINGSA NFSFNDEEMK
NVMDSSNGLS EYLDLSSPGP VEILTTVTES VTGISRNVST NVFFKQHDYI IEFFDYTTVL
KPSLNFTATV KVTRADGNQL TLEERRNNVV ITVTQRNYTE YWSGSNSGNQ KMEAVQKINY
TVPQSGTFKI EFPILEDSSE LQLKAYFLGS KSSMAVHSLF KSPSKTYIQL KTRDENIKVG
SPFELVVSGN KRLKELSYMV VSRGQLVAVG KQNSTMFSLT PENSWTPKAC VIVYYIEDDG
EIISDVLKIP VQLVFKNKIK LYWSKVKAEP SEKVSLRISV TQPDSIVGIV AVDKSVNLMN
ASNDITMENV VHELELYNTG YYLGMFMNSF AVFQECGLWV LTDANLTKDY IDGVYDNAEY
AERFMEENEG HIVDIHDFSL GSSPHVRKHF PETWIWLDTN MGSRIYQEFE VTVPDSITSW
VATGFVISED LGLGLTTTPV ELQAFQPFFI FLNLPYSVIR GEEFALEITI FNYLKDATEV
KVIIEKSDKF DILMTSNEIN ATGHQQTLLV PSEDGATVLF PIRPTHLGEI PITVTALSPT
ASDAVTQMIL VKAEGIEKSY SQSILLDLTD NRLQSTLKTL SFSFPPNTVT GSERVQITAI
GDVLGPSING LASLIRMPYG CGEQNMINFA PNIYILDYLT KKKQLTDNLK EKALSFMRQG
YQRELLYQRE DGSFSAFGNY DPSGSTWLSA FVLRCFLEAD PYIDIDQNVL HRTYTWLKGH
QKSNGEFWDP GRVIHSELQG GNKSPVTLTA YIVTSLLGYR KYQPNIDVQE SIHFLESEFS
RGISDNYTLA LITYALSSVG SPKAKEALNM LTWRAEQEGG MQFWVSSESK LSDSWQPRSL
DIEVAAYALL SHFLQFQTSE GIPIMRWLSR QRNSLGGFAS TQDTTVALKA LSEFAALMNT
ERTNIQVTVT GPSSPSPVKF LIDTHNRLLL QTAELAVVQP TAVNISANGF GFAICQLNVV
YNVKASGSSR RRRSIQNQEA FDLDVAVKEN KDDLNHVDLN VCTSFSGPGR SGMALMEVNL
LSGFMVPSEA ISLSETVKKV EYDHGKLNLY LDSVNETQFC VNIPAVRNFK VSNTQDASVS
IVDYYEPRRQ AVRSYNSEVK LSSCDLCSDV QGCRPCEDGA SGSHHHSSVI FIFCFKLLYF
MELWL*
speed 0.31 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: 0.999965629610522 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM020385)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:74493432A>CN/A show variant in all transcripts   IGV
HGNC symbol CD109
Ensembl transcript ID ENST00000437994
Genbank transcript ID NM_001159587
UniProt peptide Q6YHK3
alteration type single base exchange
alteration region CDS
DNA changes c.2108A>C
cDNA.2539A>C
g.87925A>C
AA changes Y703S Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 703
frameshift no
known variant Reference ID: rs10455097
databasehomozygous (C/C)heterozygousallele carriers
1000G71011621872
ExAC1599777316770

known disease mutation at this position, please check HGMD for details (HGMD ID CM020385)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.630.98
1.4660.883
(flanking)-0.4970.003
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost87922sequence motif lost- wt: tcag|TTAC
 mu: tcag.TTCC
Acc marginally increased87920wt: 0.3423 / mu: 0.3566 (marginal change - not scored)wt: TATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAGA
mu: TATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAGA		 cttc|AGTT
Acc marginally increased87921wt: 0.9590 / mu: 0.9605 (marginal change - not scored)wt: ATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAGAA
mu: ATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAGAA		 ttca|GTTA
Acc increased87919wt: 0.28 / mu: 0.35wt: TTATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAG
mu: TTATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAG		 actt|CAGT
Acc marginally increased87916wt: 0.8542 / mu: 0.8766 (marginal change - not scored)wt: TGTTTATATTTATTATCTTGACTTCAGTTACAGGATTTACC
mu: TGTTTATATTTATTATCTTGACTTCAGTTCCAGGATTTACC		 ttga|CTTC
Donor increased87916wt: 0.42 / mu: 0.62wt: TCTTGACTTCAGTTA
mu: TCTTGACTTCAGTTC		 TTGA|cttc
Acc gained879270.75mu: ATTATCTTGACTTCAGTTCCAGGATTTACCAAGAATTTGAA tcca|GGAT
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      703ETWIWLDTNMGYRIYQEFEVTVPD
mutated  not conserved    703ETWIWLDTNMGSRIYQEFEVTVP
Ptroglodytes  not conserved  ENSPTRG00000018349  703ETWIWLDTNMGSRIYQEFEVTVP
Mmulatta  not conserved  ENSMMUG00000017806  703ETWIWLDTNMGSRIYQEFEVTVP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000046186  705ETWIWLDAYMGSKIYEEFEVT
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060609  738ETWIWLDANVSDSASAVFSLTVP
Dmelanogaster  no homologue    
Celegans  not conserved  ZK337.1  755HTWIWSDLNSTSGEV-EMEIEA
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
593702REGIONBait region (approximate) (By similarity).might get lost (downstream of altered splice site)
789789CONFLICTK -> E (in Ref. 4; BAG36395).might get lost (downstream of altered splice site)
803803CONFLICTG -> S (in Ref. 2; AAN78483).might get lost (downstream of altered splice site)
921924CROSSLNKIsoglutamyl cysteine thioester (Cys-Gln) (By similarity).might get lost (downstream of altered splice site)
10461046CONFLICTV -> A (in Ref. 5; ABQ66266).might get lost (downstream of altered splice site)
10861086CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14181418CONFLICTD -> N (in Ref. 4; BAG53987).might get lost (downstream of altered splice site)
14201420LIPIDGPI-anchor amidated alanine (Potential).might get lost (downstream of altered splice site)
14211445PROPEPRemoved in mature form (Potential). /FTId=PRO_0000255946.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4287 / 4287
position (AA) of stopcodon in wt / mu AA sequence 1429 / 1429
position of stopcodon in wt / mu cDNA 4718 / 4718
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 432 / 432
chromosome 6
strand 1
last intron/exon boundary 4543
theoretical NMD boundary in CDS 4061
length of CDS 4287
coding sequence (CDS) position 2108
cDNA position
(for ins/del: last normal base / first normal base)		 2539
gDNA position
(for ins/del: last normal base / first normal base)		 87925
chromosomal position
(for ins/del: last normal base / first normal base)		 74493432
original gDNA sequence snippet TTATTATCTTGACTTCAGTTACAGGATTTACCAAGAATTTG
altered gDNA sequence snippet TTATTATCTTGACTTCAGTTCCAGGATTTACCAAGAATTTG
original cDNA sequence snippet GCTAGACACCAACATGGGTTACAGGATTTACCAAGAATTTG
altered cDNA sequence snippet GCTAGACACCAACATGGGTTCCAGGATTTACCAAGAATTTG
wildtype AA sequence MQGPPLLTAA HLLCVCTAAL AVAPGPRFLV TAPGIIRPGG NVTIGVELLE HCPSQVTVKA
ELLKTASNLT VSVLEAEGVF EKGSFKTLTL PSLPLNSADE IYELRVTGRT QDEILFSNST
RLSFETKRIS VFIQTDKALY KPKQEVKFRI VTLFSDFKPY KTSLNILIKD PKSNLIQQWL
SQQSDLGVIS KTFQLSSHPI LGDWSIQVQV NDQTYYQSFQ VSEYVLPKFE VTLQTPLYCS
MNSKHLNGTI TAKYTYGKPV KGDVTLTFLP LSFWGKKKNI TKTFKINGSA NFSFNDEEMK
NVMDSSNGLS EYLDLSSPGP VEILTTVTES VTGISRNVST NVFFKQHDYI IEFFDYTTVL
KPSLNFTATV KVTRADGNQL TLEERRNNVV ITVTQRNYTE YWSGSNSGNQ KMEAVQKINY
TVPQSGTFKI EFPILEDSSE LQLKAYFLGS KSSMAVHSLF KSPSKTYIQL KTRDENIKVG
SPFELVVSGN KRLKELSYMV VSRGQLVAVG KQNSTMFSLT PENSWTPKAC VIVYYIEDDG
EIISDVLKIP VQLVFKNKIK LYWSKVKAEP SEKVSLRISV TQPDSIVGIV AVDKSVNLMN
ASNDITMENV VHELELYNTG YYLGMFMNSF AVFQECGLWV LTDANLTKDY IDGVYDNAEY
AERFMEENEG HIVDIHDFSL GSSPHVRKHF PETWIWLDTN MGYRIYQEFE VTVPDSITSW
VATGFVISED LGLGLTTTPV ELQAFQPFFI FLNLPYSVIR GEEFALEITI FNYLKDATEV
KVIIEKSDKF DILMTSNEIN ATGHQQTLLV PSEDGATVLF PIRPTHLGEI PITVTALSPT
ASDAVTQMIL VKAEGIEKSY SQSILLDLTD NRLQSTLKTL SFSFPPNTVT GSERVQITAI
GDVLGPSING LASLIRMPYG CGEQNMINFA PNIYILDYLT KKKQLTDNLK EKALSFMRQG
YQRELLYQRE DGSFSAFGNY DPSGSTWLSA FVLRCFLEAD PYIDIDQNVL HRTYTWLKGH
QKSNGEFWDP GRVIHSELQG GNKSPVTLTA YIVTSLLGYR KYQPNIDVQE SIHFLESEFS
RGISDNYTLA LITYALSSVG SPKAKEALNM LTWRAEQEGG MQFWVSSESK LSDSWQPRSL
DIEVAAYALL SHFLQFQTSE GIPIMRWLSR QRNSLGGFAS TQDTTVALKA LSEFAALMNT
ERTNIQVTVT GPSSPSPLAV VQPTAVNISA NGFGFAICQL NVVYNVKASG SSRRRRSIQN
QEAFDLDVAV KENKDDLNHV DLNVCTSFSG PGRSGMALME VNLLSGFMVP SEAISLSETV
KKVEYDHGKL NLYLDSVNET QFCVNIPAVR NFKVSNTQDA SVSIVDYYEP RRQAVRSYNS
EVKLSSCDLC SDVQGCRPCE DGASGSHHHS SVIFIFCFKL LYFMELWL*
mutated AA sequence MQGPPLLTAA HLLCVCTAAL AVAPGPRFLV TAPGIIRPGG NVTIGVELLE HCPSQVTVKA
ELLKTASNLT VSVLEAEGVF EKGSFKTLTL PSLPLNSADE IYELRVTGRT QDEILFSNST
RLSFETKRIS VFIQTDKALY KPKQEVKFRI VTLFSDFKPY KTSLNILIKD PKSNLIQQWL
SQQSDLGVIS KTFQLSSHPI LGDWSIQVQV NDQTYYQSFQ VSEYVLPKFE VTLQTPLYCS
MNSKHLNGTI TAKYTYGKPV KGDVTLTFLP LSFWGKKKNI TKTFKINGSA NFSFNDEEMK
NVMDSSNGLS EYLDLSSPGP VEILTTVTES VTGISRNVST NVFFKQHDYI IEFFDYTTVL
KPSLNFTATV KVTRADGNQL TLEERRNNVV ITVTQRNYTE YWSGSNSGNQ KMEAVQKINY
TVPQSGTFKI EFPILEDSSE LQLKAYFLGS KSSMAVHSLF KSPSKTYIQL KTRDENIKVG
SPFELVVSGN KRLKELSYMV VSRGQLVAVG KQNSTMFSLT PENSWTPKAC VIVYYIEDDG
EIISDVLKIP VQLVFKNKIK LYWSKVKAEP SEKVSLRISV TQPDSIVGIV AVDKSVNLMN
ASNDITMENV VHELELYNTG YYLGMFMNSF AVFQECGLWV LTDANLTKDY IDGVYDNAEY
AERFMEENEG HIVDIHDFSL GSSPHVRKHF PETWIWLDTN MGSRIYQEFE VTVPDSITSW
VATGFVISED LGLGLTTTPV ELQAFQPFFI FLNLPYSVIR GEEFALEITI FNYLKDATEV
KVIIEKSDKF DILMTSNEIN ATGHQQTLLV PSEDGATVLF PIRPTHLGEI PITVTALSPT
ASDAVTQMIL VKAEGIEKSY SQSILLDLTD NRLQSTLKTL SFSFPPNTVT GSERVQITAI
GDVLGPSING LASLIRMPYG CGEQNMINFA PNIYILDYLT KKKQLTDNLK EKALSFMRQG
YQRELLYQRE DGSFSAFGNY DPSGSTWLSA FVLRCFLEAD PYIDIDQNVL HRTYTWLKGH
QKSNGEFWDP GRVIHSELQG GNKSPVTLTA YIVTSLLGYR KYQPNIDVQE SIHFLESEFS
RGISDNYTLA LITYALSSVG SPKAKEALNM LTWRAEQEGG MQFWVSSESK LSDSWQPRSL
DIEVAAYALL SHFLQFQTSE GIPIMRWLSR QRNSLGGFAS TQDTTVALKA LSEFAALMNT
ERTNIQVTVT GPSSPSPLAV VQPTAVNISA NGFGFAICQL NVVYNVKASG SSRRRRSIQN
QEAFDLDVAV KENKDDLNHV DLNVCTSFSG PGRSGMALME VNLLSGFMVP SEAISLSETV
KKVEYDHGKL NLYLDSVNET QFCVNIPAVR NFKVSNTQDA SVSIVDYYEP RRQAVRSYNS
EVKLSSCDLC SDVQGCRPCE DGASGSHHHS SVIFIFCFKL LYFMELWL*
speed 0.32 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: 0.999955247347919 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM020385)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:74493432A>CN/A show variant in all transcripts   IGV
HGNC symbol CD109
Ensembl transcript ID ENST00000422508
Genbank transcript ID NM_001159588
UniProt peptide Q6YHK3
alteration type single base exchange
alteration region CDS
DNA changes c.1877A>C
cDNA.2308A>C
g.87925A>C
AA changes Y626S Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 626
frameshift no
known variant Reference ID: rs10455097
databasehomozygous (C/C)heterozygousallele carriers
1000G71011621872
ExAC1599777316770

known disease mutation at this position, please check HGMD for details (HGMD ID CM020385)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.630.98
1.4660.883
(flanking)-0.4970.003
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost87922sequence motif lost- wt: tcag|TTAC
 mu: tcag.TTCC
Acc marginally increased87920wt: 0.3423 / mu: 0.3566 (marginal change - not scored)wt: TATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAGA
mu: TATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAGA		 cttc|AGTT
Acc marginally increased87921wt: 0.9590 / mu: 0.9605 (marginal change - not scored)wt: ATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAGAA
mu: ATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAGAA		 ttca|GTTA
Acc increased87919wt: 0.28 / mu: 0.35wt: TTATATTTATTATCTTGACTTCAGTTACAGGATTTACCAAG
mu: TTATATTTATTATCTTGACTTCAGTTCCAGGATTTACCAAG		 actt|CAGT
Acc marginally increased87916wt: 0.8542 / mu: 0.8766 (marginal change - not scored)wt: TGTTTATATTTATTATCTTGACTTCAGTTACAGGATTTACC
mu: TGTTTATATTTATTATCTTGACTTCAGTTCCAGGATTTACC		 ttga|CTTC
Donor increased87916wt: 0.42 / mu: 0.62wt: TCTTGACTTCAGTTA
mu: TCTTGACTTCAGTTC		 TTGA|cttc
Acc gained879270.75mu: ATTATCTTGACTTCAGTTCCAGGATTTACCAAGAATTTGAA tcca|GGAT
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      626ETWIWLDTNMGYRIYQEFEVTVPD
mutated  not conserved    626ETWIWLDTNMGSRIYQEFEVTVP
Ptroglodytes  not conserved  ENSPTRG00000018349  703ETWIWLDTNMGSRIY
Mmulatta  not conserved  ENSMMUG00000017806  703ETWIWLDTNMGSRIY
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000046186  705ETWIWLDAYMGSKIYEEFEVTV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060609  738ETWIWLDANVSDSASAVFSLTVP
Dmelanogaster  no homologue    
Celegans  not conserved  ZK337.1  755HTWIWSDLNSTSGEV-EMEIEAP
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
593702REGIONBait region (approximate) (By similarity).lost
627627CONFLICTM -> I (in Ref. 2; AAN78483).might get lost (downstream of altered splice site)
645645CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
789789CONFLICTK -> E (in Ref. 4; BAG36395).might get lost (downstream of altered splice site)
803803CONFLICTG -> S (in Ref. 2; AAN78483).might get lost (downstream of altered splice site)
921924CROSSLNKIsoglutamyl cysteine thioester (Cys-Gln) (By similarity).might get lost (downstream of altered splice site)
10461046CONFLICTV -> A (in Ref. 5; ABQ66266).might get lost (downstream of altered splice site)
10861086CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14181418CONFLICTD -> N (in Ref. 4; BAG53987).might get lost (downstream of altered splice site)
14201420LIPIDGPI-anchor amidated alanine (Potential).might get lost (downstream of altered splice site)
14211445PROPEPRemoved in mature form (Potential). /FTId=PRO_0000255946.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4107 / 4107
position (AA) of stopcodon in wt / mu AA sequence 1369 / 1369
position of stopcodon in wt / mu cDNA 4538 / 4538
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 432 / 432
chromosome 6
strand 1
last intron/exon boundary 4363
theoretical NMD boundary in CDS 3881
length of CDS 4107
coding sequence (CDS) position 1877
cDNA position
(for ins/del: last normal base / first normal base)		 2308
gDNA position
(for ins/del: last normal base / first normal base)		 87925
chromosomal position
(for ins/del: last normal base / first normal base)		 74493432
original gDNA sequence snippet TTATTATCTTGACTTCAGTTACAGGATTTACCAAGAATTTG
altered gDNA sequence snippet TTATTATCTTGACTTCAGTTCCAGGATTTACCAAGAATTTG
original cDNA sequence snippet GCTAGACACCAACATGGGTTACAGGATTTACCAAGAATTTG
altered cDNA sequence snippet GCTAGACACCAACATGGGTTCCAGGATTTACCAAGAATTTG
wildtype AA sequence MQGPPLLTAA HLLCVCTAAL AVAPGPRFLV TAPGIIRPGG NVTIGVELLE HCPSQVTVKA
ELLKTASNLT VSVLEAEGVF EKGSFKTLTL PSDPKSNLIQ QWLSQQSDLG VISKTFQLSS
HPILGDWSIQ VQVNDQTYYQ SFQVSEYVLP KFEVTLQTPL YCSMNSKHLN GTITAKYTYG
KPVKGDVTLT FLPLSFWGKK KNITKTFKIN GSANFSFNDE EMKNVMDSSN GLSEYLDLSS
PGPVEILTTV TESVTGISRN VSTNVFFKQH DYIIEFFDYT TVLKPSLNFT ATVKVTRADG
NQLTLEERRN NVVITVTQRN YTEYWSGSNS GNQKMEAVQK INYTVPQSGT FKIEFPILED
SSELQLKAYF LGSKSSMAVH SLFKSPSKTY IQLKTRDENI KVGSPFELVV SGNKRLKELS
YMVVSRGQLV AVGKQNSTMF SLTPENSWTP KACVIVYYIE DDGEIISDVL KIPVQLVFKN
KIKLYWSKVK AEPSEKVSLR ISVTQPDSIV GIVAVDKSVN LMNASNDITM ENVVHELELY
NTGYYLGMFM NSFAVFQECG LWVLTDANLT KDYIDGVYDN AEYAERFMEE NEGHIVDIHD
FSLGSSPHVR KHFPETWIWL DTNMGYRIYQ EFEVTVPDSI TSWVATGFVI SEDLGLGLTT
TPVELQAFQP FFIFLNLPYS VIRGEEFALE ITIFNYLKDA TEVKVIIEKS DKFDILMTSN
EINATGHQQT LLVPSEDGAT VLFPIRPTHL GEIPITVTAL SPTASDAVTQ MILVKAEGIE
KSYSQSILLD LTDNRLQSTL KTLSFSFPPN TVTGSERVQI TAIGDVLGPS INGLASLIRM
PYGCGEQNMI NFAPNIYILD YLTKKKQLTD NLKEKALSFM RQGYQRELLY QREDGSFSAF
GNYDPSGSTW LSAFVLRCFL EADPYIDIDQ NVLHRTYTWL KGHQKSNGEF WDPGRVIHSE
LQGGNKSPVT LTAYIVTSLL GYRKYQPNID VQESIHFLES EFSRGISDNY TLALITYALS
SVGSPKAKEA LNMLTWRAEQ EGGMQFWVSS ESKLSDSWQP RSLDIEVAAY ALLSHFLQFQ
TSEGIPIMRW LSRQRNSLGG FASTQDTTVA LKALSEFAAL MNTERTNIQV TVTGPSSPSP
VKFLIDTHNR LLLQTAELAV VQPTAVNISA NGFGFAICQL NVVYNVKASG SSRRRRSIQN
QEAFDLDVAV KENKDDLNHV DLNVCTSFSG PGRSGMALME VNLLSGFMVP SEAISLSETV
KKVEYDHGKL NLYLDSVNET QFCVNIPAVR NFKVSNTQDA SVSIVDYYEP RRQAVRSYNS
EVKLSSCDLC SDVQGCRPCE DGASGSHHHS SVIFIFCFKL LYFMELWL*
mutated AA sequence MQGPPLLTAA HLLCVCTAAL AVAPGPRFLV TAPGIIRPGG NVTIGVELLE HCPSQVTVKA
ELLKTASNLT VSVLEAEGVF EKGSFKTLTL PSDPKSNLIQ QWLSQQSDLG VISKTFQLSS
HPILGDWSIQ VQVNDQTYYQ SFQVSEYVLP KFEVTLQTPL YCSMNSKHLN GTITAKYTYG
KPVKGDVTLT FLPLSFWGKK KNITKTFKIN GSANFSFNDE EMKNVMDSSN GLSEYLDLSS
PGPVEILTTV TESVTGISRN VSTNVFFKQH DYIIEFFDYT TVLKPSLNFT ATVKVTRADG
NQLTLEERRN NVVITVTQRN YTEYWSGSNS GNQKMEAVQK INYTVPQSGT FKIEFPILED
SSELQLKAYF LGSKSSMAVH SLFKSPSKTY IQLKTRDENI KVGSPFELVV SGNKRLKELS
YMVVSRGQLV AVGKQNSTMF SLTPENSWTP KACVIVYYIE DDGEIISDVL KIPVQLVFKN
KIKLYWSKVK AEPSEKVSLR ISVTQPDSIV GIVAVDKSVN LMNASNDITM ENVVHELELY
NTGYYLGMFM NSFAVFQECG LWVLTDANLT KDYIDGVYDN AEYAERFMEE NEGHIVDIHD
FSLGSSPHVR KHFPETWIWL DTNMGSRIYQ EFEVTVPDSI TSWVATGFVI SEDLGLGLTT
TPVELQAFQP FFIFLNLPYS VIRGEEFALE ITIFNYLKDA TEVKVIIEKS DKFDILMTSN
EINATGHQQT LLVPSEDGAT VLFPIRPTHL GEIPITVTAL SPTASDAVTQ MILVKAEGIE
KSYSQSILLD LTDNRLQSTL KTLSFSFPPN TVTGSERVQI TAIGDVLGPS INGLASLIRM
PYGCGEQNMI NFAPNIYILD YLTKKKQLTD NLKEKALSFM RQGYQRELLY QREDGSFSAF
GNYDPSGSTW LSAFVLRCFL EADPYIDIDQ NVLHRTYTWL KGHQKSNGEF WDPGRVIHSE
LQGGNKSPVT LTAYIVTSLL GYRKYQPNID VQESIHFLES EFSRGISDNY TLALITYALS
SVGSPKAKEA LNMLTWRAEQ EGGMQFWVSS ESKLSDSWQP RSLDIEVAAY ALLSHFLQFQ
TSEGIPIMRW LSRQRNSLGG FASTQDTTVA LKALSEFAAL MNTERTNIQV TVTGPSSPSP
VKFLIDTHNR LLLQTAELAV VQPTAVNISA NGFGFAICQL NVVYNVKASG SSRRRRSIQN
QEAFDLDVAV KENKDDLNHV DLNVCTSFSG PGRSGMALME VNLLSGFMVP SEAISLSETV
KKVEYDHGKL NLYLDSVNET QFCVNIPAVR NFKVSNTQDA SVSIVDYYEP RRQAVRSYNS
EVKLSSCDLC SDVQGCRPCE DGASGSHHHS SVIFIFCFKL LYFMELWL*
speed 0.23 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