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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: ENST00000284425
MT speed 0 s - this script 2.84545 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCA6polymorphism_automatic9.83300108003959e-11simple_aaeaffectedV282Isingle base exchangers4968839show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999990167 (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) chr17:67125840C>TN/A show variant in all transcripts   IGV
HGNC symbol ABCA6
Ensembl transcript ID ENST00000284425
Genbank transcript ID NM_080284
UniProt peptide Q8N139
alteration type single base exchange
alteration region CDS
DNA changes c.844G>A
cDNA.1019G>A
g.12190G>A
AA changes V282I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 282
frameshift no
known variant Reference ID: rs4968839
databasehomozygous (T/T)heterozygousallele carriers
1000G85210761928
ExAC26819-208715948
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2410.124
0.2860.115
(flanking)0.2990.114
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased12193wt: 0.28 / mu: 0.48wt: TTATTATTTCCATATTCGTTACAATTATCATAACATTCACC
mu: TTATTATTTCCATATTCATTACAATTATCATAACATTCACC		 gtta|CAAT
Acc marginally increased12191wt: 0.2914 / mu: 0.3176 (marginal change - not scored)wt: CTTTATTATTTCCATATTCGTTACAATTATCATAACATTCA
mu: CTTTATTATTTCCATATTCATTACAATTATCATAACATTCA		 tcgt|TACA
Acc marginally increased12181wt: 0.8315 / mu: 0.8448 (marginal change - not scored)wt: CTGGCTTCATCTTTATTATTTCCATATTCGTTACAATTATC
mu: CTGGCTTCATCTTTATTATTTCCATATTCATTACAATTATC		 attt|CCAT
Acc marginally increased12185wt: 0.9922 / mu: 0.9928 (marginal change - not scored)wt: CTTCATCTTTATTATTTCCATATTCGTTACAATTATCATAA
mu: CTTCATCTTTATTATTTCCATATTCATTACAATTATCATAA		 ccat|ATTC
Acc marginally increased12190wt: 0.7415 / mu: 0.7762 (marginal change - not scored)wt: TCTTTATTATTTCCATATTCGTTACAATTATCATAACATTC
mu: TCTTTATTATTTCCATATTCATTACAATTATCATAACATTC		 ttcg|TTAC
Acc marginally increased12187wt: 0.4503 / mu: 0.4748 (marginal change - not scored)wt: TCATCTTTATTATTTCCATATTCGTTACAATTATCATAACA
mu: TCATCTTTATTATTTCCATATTCATTACAATTATCATAACA		 atat|TCGT
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      282YAGFIFIISIFVTIIITFTQIIVM
mutated  all conserved    282YAGFIFIISIFITIIITFTQIIV
Ptroglodytes  all identical  ENSPTRG00000009584  214SIFVTIIITFTQIIV
Mmulatta  all conserved  ENSMMUG00000018592  283YAGFIFIISIFITIVITFTEIIV
Fcatus  no alignment  ENSFCAG00000015679  n/a
Mmusculus  all conserved  ENSMUSG00000044749  282YVGFIFIISIFIAIIITSTQIIM
Ggallus  all conserved  ENSGALG00000021399  283YAIYVLVLSCPLTALV-MNETFH
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all conserved  FBgn0031170  331SFIMLTISAILIA
Celegans  all conserved  Y39D8C.1  379YAKLTFAV-IVLTI
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
268288TRANSMEMHelical; (Potential).lost
297317TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
327347TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
355375TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
397417TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
478713DOMAINABC transporter 1.might get lost (downstream of altered splice site)
514521NP_BINDATP 1 (Potential).might get lost (downstream of altered splice site)
812812CONFLICTE -> G (in Ref. 4; BAC04994).might get lost (downstream of altered splice site)
854874TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
875876CONFLICTMY -> IH (in Ref. 4; BAC04994).might get lost (downstream of altered splice site)
940940CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
10071027TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10621082TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10941114TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
11271147TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
11501170TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
11941214TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
12881513DOMAINABC transporter 2.might get lost (downstream of altered splice site)
13201327NP_BINDATP 2 (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4854 / 4854
position (AA) of stopcodon in wt / mu AA sequence 1618 / 1618
position of stopcodon in wt / mu cDNA 5029 / 5029
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 176 / 176
chromosome 17
strand -1
last intron/exon boundary 4928
theoretical NMD boundary in CDS 4702
length of CDS 4854
coding sequence (CDS) position 844
cDNA position
(for ins/del: last normal base / first normal base)		 1019
gDNA position
(for ins/del: last normal base / first normal base)		 12190
chromosomal position
(for ins/del: last normal base / first normal base)		 67125840
original gDNA sequence snippet TCTTTATTATTTCCATATTCGTTACAATTATCATAACATTC
altered gDNA sequence snippet TCTTTATTATTTCCATATTCATTACAATTATCATAACATTC
original cDNA sequence snippet TCTTTATTATTTCCATATTCGTTACAATTATCATAACATTC
altered cDNA sequence snippet TCTTTATTATTTCCATATTCATTACAATTATCATAACATTC
wildtype AA sequence MNMKQKSVYQ QTKALLCKNF LKKWRMKRES LLEWGLSILL GLCIALFSSS MRNVQFPGMA
PQNLGRVDKF NSSSLMVVYT PISNLTQQIM NKTALAPLLK GTSVIGAPNK THMDEILLEN
LPYAMGIIFN ETFSYKLIFF QGYNSPLWKE DFSAHCWDGY GEFSCTLTKY WNRGFVALQT
AINTAIIEIT TNHPVMEELM SVTAITMKTL PFITKNLLHN EMFILFFLLH FSPLVYFISL
NVTKERKKSK NLMKMMGLQD SAFWLSWGLI YAGFIFIISI FVTIIITFTQ IIVMTGFMVI
FILFFLYGLS LVALVFLMSV LLKKAVLTNL VVFLLTLFWG CLGFTVFYEQ LPSSLEWILN
ICSPFAFTTG MIQIIKLDYN LNGVIFPDPS GDSYTMIATF SMLLLDGLIY LLLALYFDKI
LPYGDERHYS PLFFLNSSSC FQHQRTNAKV IEKEIDAEHP SDDYFEPVAP EFQGKEAIRI
RNVKKEYKGK SGKVEALKGL LFDIYEGQIT AILGHSGAGK SSLLNILNGL SVPTEGSVTI
YNKNLSEMQD LEEIRKITGV CPQFNVQFDI LTVKENLSLF AKIKGIHLKE VEQEVQRILL
ELDMQNIQDN LAKHLSEGQK RKLTFGITIL GDPQILLLDE PTTGLDPFSR DQVWSLLRER
RADHVILFST QSMDEADILA DRKVIMSNGR LKCAGSSMFL KRRWGLGYHL SLHRNEICNP
EQITSFITHH IPDAKLKTEN KEKLVYTLPL ERTNTFPDLF SDLDKCSDQG VTGYDISMST
LNEVFMKLEG QSTIEQDFEQ VEMIRDSESL NEMELAHSSF SEMQTAVSDM GLWRMQVFAM
ARLRFLKLKR QTKVLLTLLL VFGIAIFPLI VENIMYAMLN EKIDWEFKNE LYFLSPGQLP
QEPRTSLLII NNTESNIEDF IKSLKHQNIL LEVDDFENRN GTDGLSYNGA IIVSGKQKDY
RFSVVCNTKR LHCFPILMNI ISNGLLQMFN HTQHIRIESS PFPLSHIGLW TGLPDGSFFL
FLVLCSISPY ITMGSISDYK KNAKSQLWIS GLYTSAYWCG QALVDVSFFI LILLLMYLIF
YIENMQYLLI TSQIVFALVI VTPGYAASLV FFIYMISFIF RKRRKNSGLW SFYFFFASTI
MFSITLINHF DLSILITTMV LVPSYTLLGF KTFLEVRDQE HYREFPEANF ELSATDFLVC
FIPYFQTLLF VFVLRCMELK CGKKRMRKDP VFRISPQSRD AKPNPEEPID EDEDIQTERI
RTATALTTSI LDEKPVIIAS CLHKEYAGQK KSCFSKRKKK IAARNISFCV QEGEILGLLG
PNGAGKSSSI RMISGITKPT AGEVELKGCS SVLGHLGYCP QENVLWPMLT LREHLEVYAA
VKGLRKADAR LAIARLVSAF KLHEQLNVPV QKLTAGITRK LCFVLSLLGN SPVLLLDEPS
TGIDPTGQQQ MWQAIQAVVK NTERGVLLTT HNLAEAEALC DRVAIMVSGR LRCIGSIQHL
KNKLGKDYIL ELKVKETSQV TLVHTEILKL FPQAAGQERY SSLLTYKLPV ADVYPLSQTF
HKLEAVKHNF NLEEYSLSQC TLEKVFLELS KEQEVGNFDE EIDTTMRWKL LPHSDEP*
mutated AA sequence MNMKQKSVYQ QTKALLCKNF LKKWRMKRES LLEWGLSILL GLCIALFSSS MRNVQFPGMA
PQNLGRVDKF NSSSLMVVYT PISNLTQQIM NKTALAPLLK GTSVIGAPNK THMDEILLEN
LPYAMGIIFN ETFSYKLIFF QGYNSPLWKE DFSAHCWDGY GEFSCTLTKY WNRGFVALQT
AINTAIIEIT TNHPVMEELM SVTAITMKTL PFITKNLLHN EMFILFFLLH FSPLVYFISL
NVTKERKKSK NLMKMMGLQD SAFWLSWGLI YAGFIFIISI FITIIITFTQ IIVMTGFMVI
FILFFLYGLS LVALVFLMSV LLKKAVLTNL VVFLLTLFWG CLGFTVFYEQ LPSSLEWILN
ICSPFAFTTG MIQIIKLDYN LNGVIFPDPS GDSYTMIATF SMLLLDGLIY LLLALYFDKI
LPYGDERHYS PLFFLNSSSC FQHQRTNAKV IEKEIDAEHP SDDYFEPVAP EFQGKEAIRI
RNVKKEYKGK SGKVEALKGL LFDIYEGQIT AILGHSGAGK SSLLNILNGL SVPTEGSVTI
YNKNLSEMQD LEEIRKITGV CPQFNVQFDI LTVKENLSLF AKIKGIHLKE VEQEVQRILL
ELDMQNIQDN LAKHLSEGQK RKLTFGITIL GDPQILLLDE PTTGLDPFSR DQVWSLLRER
RADHVILFST QSMDEADILA DRKVIMSNGR LKCAGSSMFL KRRWGLGYHL SLHRNEICNP
EQITSFITHH IPDAKLKTEN KEKLVYTLPL ERTNTFPDLF SDLDKCSDQG VTGYDISMST
LNEVFMKLEG QSTIEQDFEQ VEMIRDSESL NEMELAHSSF SEMQTAVSDM GLWRMQVFAM
ARLRFLKLKR QTKVLLTLLL VFGIAIFPLI VENIMYAMLN EKIDWEFKNE LYFLSPGQLP
QEPRTSLLII NNTESNIEDF IKSLKHQNIL LEVDDFENRN GTDGLSYNGA IIVSGKQKDY
RFSVVCNTKR LHCFPILMNI ISNGLLQMFN HTQHIRIESS PFPLSHIGLW TGLPDGSFFL
FLVLCSISPY ITMGSISDYK KNAKSQLWIS GLYTSAYWCG QALVDVSFFI LILLLMYLIF
YIENMQYLLI TSQIVFALVI VTPGYAASLV FFIYMISFIF RKRRKNSGLW SFYFFFASTI
MFSITLINHF DLSILITTMV LVPSYTLLGF KTFLEVRDQE HYREFPEANF ELSATDFLVC
FIPYFQTLLF VFVLRCMELK CGKKRMRKDP VFRISPQSRD AKPNPEEPID EDEDIQTERI
RTATALTTSI LDEKPVIIAS CLHKEYAGQK KSCFSKRKKK IAARNISFCV QEGEILGLLG
PNGAGKSSSI RMISGITKPT AGEVELKGCS SVLGHLGYCP QENVLWPMLT LREHLEVYAA
VKGLRKADAR LAIARLVSAF KLHEQLNVPV QKLTAGITRK LCFVLSLLGN SPVLLLDEPS
TGIDPTGQQQ MWQAIQAVVK NTERGVLLTT HNLAEAEALC DRVAIMVSGR LRCIGSIQHL
KNKLGKDYIL ELKVKETSQV TLVHTEILKL FPQAAGQERY SSLLTYKLPV ADVYPLSQTF
HKLEAVKHNF NLEEYSLSQC TLEKVFLELS KEQEVGNFDE EIDTTMRWKL LPHSDEP*
speed 0.78 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