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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000374736
MT speed 0 s - this script 3.529251 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCA1disease_causing_automatic0.999999093007665simple_aaeaffected0Q597Rsingle base exchangers2853578show file

Taster files

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mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999093007665 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990003)
  • known disease mutation: rs9485 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:107593308T>CN/A show variant in all transcripts   IGV
HGNC symbol ABCA1
Ensembl transcript ID ENST00000374736
Genbank transcript ID NM_005502
UniProt peptide O95477
alteration type single base exchange
alteration region CDS
DNA changes c.1790A>G
cDNA.2185A>G
g.97211A>G
AA changes Q597R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 597
frameshift no
known variant Reference ID: rs2853578
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9485 (pathogenic for Tangier disease) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990003)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990003)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990003)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5951
5.2061
(flanking)6.3041
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased97210wt: 0.26 / mu: 0.57wt: GGGGGGGCTTCGCCTACTTGCAGGATGTGGTGGAGCAGGCA
mu: GGGGGGGCTTCGCCTACTTGCGGGATGTGGTGGAGCAGGCA		 ttgc|AGGA
Acc marginally increased97212wt: 0.7421 / mu: 0.7445 (marginal change - not scored)wt: GGGGGCTTCGCCTACTTGCAGGATGTGGTGGAGCAGGCAAT
mu: GGGGGCTTCGCCTACTTGCGGGATGTGGTGGAGCAGGCAAT		 gcag|GATG
Acc marginally increased97217wt: 0.3777 / mu: 0.3784 (marginal change - not scored)wt: CTTCGCCTACTTGCAGGATGTGGTGGAGCAGGCAATCATCA
mu: CTTCGCCTACTTGCGGGATGTGGTGGAGCAGGCAATCATCA		 atgt|GGTG
Donor gained972100.94mu: ACTTGCGGGATGTGG TTGC|ggga
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      597MRYVWGGFAYLQDVVEQAIIRVLT
mutated  all conserved    597MRYVWGGFAYLRDVV
Ptroglodytes  all identical  ENSPTRG00000021219  597MRYVWGGFAYLQDVV
Mmulatta  no alignment  ENSMMUG00000020608  n/a
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000015243  597MRYVWGGFAYLQDVV
Ggallus  all identical  ENSGALG00000015433  600YLQDVVEQAIIRVQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074635  601TYLQDVIEHGIIRAL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000000951  601QDVVEQAIIRVQ
protein features
start (aa)end (aa)featuredetails 
43639TOPO_DOMExtracellular.lost
640660TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
683703TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
716736TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
745765TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
777797TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
793793CONFLICTY -> C (in Ref. 3; AAK43526).might get lost (downstream of altered splice site)
820820CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
827847TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
831831CONFLICTD -> N (in Ref. 3; AAK43526).might get lost (downstream of altered splice site)
8991131DOMAINABC transporter 1.might get lost (downstream of altered splice site)
933940NP_BINDATP 1 (Potential).might get lost (downstream of altered splice site)
10051005CONFLICTE -> K (in Ref. 3; AAK43526).might get lost (downstream of altered splice site)
10411057TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10421042MOD_RESPhosphoserine; by PKA.might get lost (downstream of altered splice site)
11101110LIPIDS-palmitoyl cysteine.might get lost (downstream of altered splice site)
11111111LIPIDS-palmitoyl cysteine.might get lost (downstream of altered splice site)
11411141MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
11441144CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11471147MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
12941294CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
13511371TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
13721656TOPO_DOMExtracellular.might get lost (downstream of altered splice site)
14531453CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14631463DISULFIDmight get lost (downstream of altered splice site)
14771477DISULFIDmight get lost (downstream of altered splice site)
15041504CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16371637CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16571677TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
17031723TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
17351755TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
17451746CONFLICTMissing (in Ref. 7; AAD49852).might get lost (downstream of altered splice site)
17681788TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
18021822TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
18521872TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
19122144DOMAINABC transporter 2.might get lost (downstream of altered splice site)
19461953NP_BINDATP 2 (Potential).might get lost (downstream of altered splice site)
20442044CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
20542054MOD_RESPhosphoserine; by PKA.might get lost (downstream of altered splice site)
22382238CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6786 / 6786
position (AA) of stopcodon in wt / mu AA sequence 2262 / 2262
position of stopcodon in wt / mu cDNA 7181 / 7181
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 396 / 396
chromosome 9
strand -1
last intron/exon boundary 7041
theoretical NMD boundary in CDS 6595
length of CDS 6786
coding sequence (CDS) position 1790
cDNA position
(for ins/del: last normal base / first normal base)		 2185
gDNA position
(for ins/del: last normal base / first normal base)		 97211
chromosomal position
(for ins/del: last normal base / first normal base)		 107593308
original gDNA sequence snippet GGGGGGCTTCGCCTACTTGCAGGATGTGGTGGAGCAGGCAA
altered gDNA sequence snippet GGGGGGCTTCGCCTACTTGCGGGATGTGGTGGAGCAGGCAA
original cDNA sequence snippet GGGGGGCTTCGCCTACTTGCAGGATGTGGTGGAGCAGGCAA
altered cDNA sequence snippet GGGGGGCTTCGCCTACTTGCGGGATGTGGTGGAGCAGGCAA
wildtype AA sequence MACWPQLRLL LWKNLTFRRR QTCQLLLEVA WPLFIFLILI SVRLSYPPYE QHECHFPNKA
MPSAGTLPWV QGIICNANNP CFRYPTPGEA PGVVGNFNKS IVARLFSDAR RLLLYSQKDT
SMKDMRKVLR TLQQIKKSSS NLKLQDFLVD NETFSGFLYH NLSLPKSTVD KMLRADVILH
KVFLQGYQLH LTSLCNGSKS EEMIQLGDQE VSELCGLPRE KLAAAERVLR SNMDILKPIL
RTLNSTSPFP SKELAEATKT LLHSLGTLAQ ELFSMRSWSD MRQEVMFLTN VNSSSSSTQI
YQAVSRIVCG HPEGGGLKIK SLNWYEDNNY KALFGGNGTE EDAETFYDNS TTPYCNDLMK
NLESSPLSRI IWKALKPLLV GKILYTPDTP ATRQVMAEVN KTFQELAVFH DLEGMWEELS
PKIWTFMENS QEMDLVRMLL DSRDNDHFWE QQLDGLDWTA QDIVAFLAKH PEDVQSSNGS
VYTWREAFNE TNQAIRTISR FMECVNLNKL EPIATEVWLI NKSMELLDER KFWAGIVFTG
ITPGSIELPH HVKYKIRMDI DNVERTNKIK DGYWDPGPRA DPFEDMRYVW GGFAYLQDVV
EQAIIRVLTG TEKKTGVYMQ QMPYPCYVDD IFLRVMSRSM PLFMTLAWIY SVAVIIKGIV
YEKEARLKET MRIMGLDNSI LWFSWFISSL IPLLVSAGLL VVILKLGNLL PYSDPSVVFV
FLSVFAVVTI LQCFLISTLF SRANLAAACG GIIYFTLYLP YVLCVAWQDY VGFTLKIFAS
LLSPVAFGFG CEYFALFEEQ GIGVQWDNLF ESPVEEDGFN LTTSVSMMLF DTFLYGVMTW
YIEAVFPGQY GIPRPWYFPC TKSYWFGEES DEKSHPGSNQ KRISEICMEE EPTHLKLGVS
IQNLVKVYRD GMKVAVDGLA LNFYEGQITS FLGHNGAGKT TTMSILTGLF PPTSGTAYIL
GKDIRSEMST IRQNLGVCPQ HNVLFDMLTV EEHIWFYARL KGLSEKHVKA EMEQMALDVG
LPSSKLKSKT SQLSGGMQRK LSVALAFVGG SKVVILDEPT AGVDPYSRRG IWELLLKYRQ
GRTIILSTHH MDEADVLGDR IAIISHGKLC CVGSSLFLKN QLGTGYYLTL VKKDVESSLS
SCRNSSSTVS YLKKEDSVSQ SSSDAGLGSD HESDTLTIDV SAISNLIRKH VSEARLVEDI
GHELTYVLPY EAAKEGAFVE LFHEIDDRLS DLGISSYGIS ETTLEEIFLK VAEESGVDAE
TSDGTLPARR NRRAFGDKQS CLRPFTEDDA ADPNDSDIDP ESRETDLLSG MDGKGSYQVK
GWKLTQQQFV ALLWKRLLIA RRSRKGFFAQ IVLPAVFVCI ALVFSLIVPP FGKYPSLELQ
PWMYNEQYTF VSNDAPEDTG TLELLNALTK DPGFGTRCME GNPIPDTPCQ AGEEEWTTAP
VPQTIMDLFQ NGNWTMQNPS PACQCSSDKI KKMLPVCPPG AGGLPPPQRK QNTADILQDL
TGRNISDYLV KTYVQIIAKS LKNKIWVNEF RYGGFSLGVS NTQALPPSQE VNDAIKQMKK
HLKLAKDSSA DRFLNSLGRF MTGLDTKNNV KVWFNNKGWH AISSFLNVIN NAILRANLQK
GENPSHYGIT AFNHPLNLTK QQLSEVALMT TSVDVLVSIC VIFAMSFVPA SFVVFLIQER
VSKAKHLQFI SGVKPVIYWL SNFVWDMCNY VVPATLVIII FICFQQKSYV SSTNLPVLAL
LLLLYGWSIT PLMYPASFVF KIPSTAYVVL TSVNLFIGIN GSVATFVLEL FTDNKLNNIN
DILKSVFLIF PHFCLGRGLI DMVKNQAMAD ALERFGENRF VSPLSWDLVG RNLFAMAVEG
VVFFLITVLI QYRFFIRPRP VNAKLSPLND EDEDVRRERQ RILDGGGQND ILEIKELTKI
YRRKRKPAVD RICVGIPPGE CFGLLGVNGA GKSSTFKMLT GDTTVTRGDA FLNKNSILSN
IHEVHQNMGY CPQFDAITEL LTGREHVEFF ALLRGVPEKE VGKVGEWAIR KLGLVKYGEK
YAGNYSGGNK RKLSTAMALI GGPPVVFLDE PTTGMDPKAR RFLWNCALSV VKEGRSVVLT
SHSMEECEAL CTRMAIMVNG RFRCLGSVQH LKNRFGDGYT IVVRIAGSNP DLKPVQDFFG
LAFPGSVLKE KHRNMLQYQL PSSLSSLARI FSILSQSKKR LHIEDYSVSQ TTLDQVFVNF
AKDQSDDDHL KDLSLHKNQT VVDVAVLTSF LQDEKVKESY V*
mutated AA sequence MACWPQLRLL LWKNLTFRRR QTCQLLLEVA WPLFIFLILI SVRLSYPPYE QHECHFPNKA
MPSAGTLPWV QGIICNANNP CFRYPTPGEA PGVVGNFNKS IVARLFSDAR RLLLYSQKDT
SMKDMRKVLR TLQQIKKSSS NLKLQDFLVD NETFSGFLYH NLSLPKSTVD KMLRADVILH
KVFLQGYQLH LTSLCNGSKS EEMIQLGDQE VSELCGLPRE KLAAAERVLR SNMDILKPIL
RTLNSTSPFP SKELAEATKT LLHSLGTLAQ ELFSMRSWSD MRQEVMFLTN VNSSSSSTQI
YQAVSRIVCG HPEGGGLKIK SLNWYEDNNY KALFGGNGTE EDAETFYDNS TTPYCNDLMK
NLESSPLSRI IWKALKPLLV GKILYTPDTP ATRQVMAEVN KTFQELAVFH DLEGMWEELS
PKIWTFMENS QEMDLVRMLL DSRDNDHFWE QQLDGLDWTA QDIVAFLAKH PEDVQSSNGS
VYTWREAFNE TNQAIRTISR FMECVNLNKL EPIATEVWLI NKSMELLDER KFWAGIVFTG
ITPGSIELPH HVKYKIRMDI DNVERTNKIK DGYWDPGPRA DPFEDMRYVW GGFAYLRDVV
EQAIIRVLTG TEKKTGVYMQ QMPYPCYVDD IFLRVMSRSM PLFMTLAWIY SVAVIIKGIV
YEKEARLKET MRIMGLDNSI LWFSWFISSL IPLLVSAGLL VVILKLGNLL PYSDPSVVFV
FLSVFAVVTI LQCFLISTLF SRANLAAACG GIIYFTLYLP YVLCVAWQDY VGFTLKIFAS
LLSPVAFGFG CEYFALFEEQ GIGVQWDNLF ESPVEEDGFN LTTSVSMMLF DTFLYGVMTW
YIEAVFPGQY GIPRPWYFPC TKSYWFGEES DEKSHPGSNQ KRISEICMEE EPTHLKLGVS
IQNLVKVYRD GMKVAVDGLA LNFYEGQITS FLGHNGAGKT TTMSILTGLF PPTSGTAYIL
GKDIRSEMST IRQNLGVCPQ HNVLFDMLTV EEHIWFYARL KGLSEKHVKA EMEQMALDVG
LPSSKLKSKT SQLSGGMQRK LSVALAFVGG SKVVILDEPT AGVDPYSRRG IWELLLKYRQ
GRTIILSTHH MDEADVLGDR IAIISHGKLC CVGSSLFLKN QLGTGYYLTL VKKDVESSLS
SCRNSSSTVS YLKKEDSVSQ SSSDAGLGSD HESDTLTIDV SAISNLIRKH VSEARLVEDI
GHELTYVLPY EAAKEGAFVE LFHEIDDRLS DLGISSYGIS ETTLEEIFLK VAEESGVDAE
TSDGTLPARR NRRAFGDKQS CLRPFTEDDA ADPNDSDIDP ESRETDLLSG MDGKGSYQVK
GWKLTQQQFV ALLWKRLLIA RRSRKGFFAQ IVLPAVFVCI ALVFSLIVPP FGKYPSLELQ
PWMYNEQYTF VSNDAPEDTG TLELLNALTK DPGFGTRCME GNPIPDTPCQ AGEEEWTTAP
VPQTIMDLFQ NGNWTMQNPS PACQCSSDKI KKMLPVCPPG AGGLPPPQRK QNTADILQDL
TGRNISDYLV KTYVQIIAKS LKNKIWVNEF RYGGFSLGVS NTQALPPSQE VNDAIKQMKK
HLKLAKDSSA DRFLNSLGRF MTGLDTKNNV KVWFNNKGWH AISSFLNVIN NAILRANLQK
GENPSHYGIT AFNHPLNLTK QQLSEVALMT TSVDVLVSIC VIFAMSFVPA SFVVFLIQER
VSKAKHLQFI SGVKPVIYWL SNFVWDMCNY VVPATLVIII FICFQQKSYV SSTNLPVLAL
LLLLYGWSIT PLMYPASFVF KIPSTAYVVL TSVNLFIGIN GSVATFVLEL FTDNKLNNIN
DILKSVFLIF PHFCLGRGLI DMVKNQAMAD ALERFGENRF VSPLSWDLVG RNLFAMAVEG
VVFFLITVLI QYRFFIRPRP VNAKLSPLND EDEDVRRERQ RILDGGGQND ILEIKELTKI
YRRKRKPAVD RICVGIPPGE CFGLLGVNGA GKSSTFKMLT GDTTVTRGDA FLNKNSILSN
IHEVHQNMGY CPQFDAITEL LTGREHVEFF ALLRGVPEKE VGKVGEWAIR KLGLVKYGEK
YAGNYSGGNK RKLSTAMALI GGPPVVFLDE PTTGMDPKAR RFLWNCALSV VKEGRSVVLT
SHSMEECEAL CTRMAIMVNG RFRCLGSVQH LKNRFGDGYT IVVRIAGSNP DLKPVQDFFG
LAFPGSVLKE KHRNMLQYQL PSSLSSLARI FSILSQSKKR LHIEDYSVSQ TTLDQVFVNF
AKDQSDDDHL KDLSLHKNQT VVDVAVLTSF LQDEKVKESY V*
speed 1.36 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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