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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000370225
MT speed 0 s - this script 2.938828 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCA4disease_causing_automatic0.430443330065533simple_aaeaffected0E1036Ksingle base exchangers61750061show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.430443330065533 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980006)
  • known disease mutation: rs7886 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:94508976C>TN/A show variant in all transcripts   IGV
HGNC symbol ABCA4
Ensembl transcript ID ENST00000370225
Genbank transcript ID NM_000350
UniProt peptide P78363
alteration type single base exchange
alteration region CDS
DNA changes c.3106G>A
cDNA.3193G>A
g.77713G>A
AA changes E1036K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1036
frameshift no
known variant Reference ID: rs61750061
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7886 (pathogenic for Stargardt disease 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980006)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980006)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980006)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)2.4370.982
1.3370.958
(flanking)1.310.833
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased77709wt: 0.72 / mu: 0.94wt: AAGTCCCAGGAGGAG
mu: AAGTCCCAGAAGGAG		 GTCC|cagg
Donor gained777130.44mu: CCCAGAAGGAGGCCC CAGA|agga
distance from splice site 56
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1036LFYAQLKGKSQEEAQLEMEAMLED
mutated  all conserved    1036LFYAQLKGKSQKEAQLEMEAMLE
Ptroglodytes  all identical  ENSPTRG00000023377  1036LFYAQLKGKSQEEAQLEMEAMLE
Mmulatta  all identical  ENSMMUG00000013858  1036LFYAQLKGKSWEEAQLEMEAMLE
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028125  1036LFYAQLKGRSWEEAQLEMEAMLE
Ggallus  all conserved  ENSGALG00000005752  1037LFYSQLKGRSRDEAEQELEMMLE
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000062661  1096LFYSLMKGREHKEAEQEVENMLE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000008223  1101LFYAQLKGKSRKQAERQAEVMLE
protein features
start (aa)end (aa)featuredetails 
8571376TOPO_DOMCytoplasmic.lost
9291160DOMAINABC transporter 1.lost
11161116CONFLICTS -> P (in Ref. 1; AAC51144).might get lost (downstream of altered splice site)
11251126CONFLICTLL -> HQ (in Ref. 1; AAC51144).might get lost (downstream of altered splice site)
13771397TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
13951395CONFLICTP -> L (in Ref. 1; AAC51144 and 3; CAA75729).might get lost (downstream of altered splice site)
13981727TOPO_DOMExtracellular.might get lost (downstream of altered splice site)
14651465CONFLICTS -> C (in Ref. 4; AAC05632).might get lost (downstream of altered splice site)
14691469CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
14881488DISULFIDBy similarity.might get lost (downstream of altered splice site)
15021502DISULFIDBy similarity.might get lost (downstream of altered splice site)
15181518CONFLICTS -> T (in Ref. 4; AAC05632).might get lost (downstream of altered splice site)
15291529CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
15881588CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
16621662CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
17281748TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
17331733CONFLICTM -> V (in Ref. 2; AAC23915).might get lost (downstream of altered splice site)
17601780TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
17931813TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
18321852TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
18741894TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
18952273TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
19382170DOMAINABC transporter 2.might get lost (downstream of altered splice site)
19721979NP_BINDATP 2 (Potential).might get lost (downstream of altered splice site)
19751975MUTAGENG->D: Inhibition of retinal-stimulated ATP hydrolysis.might get lost (downstream of altered splice site)
19781978MUTAGENK->M: Inhibition of retinal-stimulated ATP hydrolysis.might get lost (downstream of altered splice site)
19891989CONFLICTT -> N (in Ref. 2; AAC23915).might get lost (downstream of altered splice site)
21192119CONFLICTE -> K (in Ref. 1; AAC51144).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6822 / 6822
position (AA) of stopcodon in wt / mu AA sequence 2274 / 2274
position of stopcodon in wt / mu cDNA 6909 / 6909
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 88 / 88
chromosome 1
strand -1
last intron/exon boundary 6904
theoretical NMD boundary in CDS 6766
length of CDS 6822
coding sequence (CDS) position 3106
cDNA position
(for ins/del: last normal base / first normal base)		 3193
gDNA position
(for ins/del: last normal base / first normal base)		 77713
chromosomal position
(for ins/del: last normal base / first normal base)		 94508976
original gDNA sequence snippet AGCTGAAAGGAAAGTCCCAGGAGGAGGCCCAGCTGGAGATG
altered gDNA sequence snippet AGCTGAAAGGAAAGTCCCAGAAGGAGGCCCAGCTGGAGATG
original cDNA sequence snippet AGCTGAAAGGAAAGTCCCAGGAGGAGGCCCAGCTGGAGATG
altered cDNA sequence snippet AGCTGAAAGGAAAGTCCCAGAAGGAGGCCCAGCTGGAGATG
wildtype AA sequence MGFVRQIQLL LWKNWTLRKR QKIRFVVELV WPLSLFLVLI WLRNANPLYS HHECHFPNKA
MPSAGMLPWL QGIFCNVNNP CFQSPTPGES PGIVSNYNNS ILARVYRDFQ ELLMNAPESQ
HLGRIWTELH ILSQFMDTLR THPERIAGRG IRIRDILKDE ETLTLFLIKN IGLSDSVVYL
LINSQVRPEQ FAHGVPDLAL KDIACSEALL ERFIIFSQRR GAKTVRYALC SLSQGTLQWI
EDTLYANVDF FKLFRVLPTL LDSRSQGINL RSWGGILSDM SPRIQEFIHR PSMQDLLWVT
RPLMQNGGPE TFTKLMGILS DLLCGYPEGG GSRVLSFNWY EDNNYKAFLG IDSTRKDPIY
SYDRRTTSFC NALIQSLESN PLTKIAWRAA KPLLMGKILY TPDSPAARRI LKNANSTFEE
LEHVRKLVKA WEEVGPQIWY FFDNSTQMNM IRDTLGNPTV KDFLNRQLGE EGITAEAILN
FLYKGPRESQ ADDMANFDWR DIFNITDRTL RLVNQYLECL VLDKFESYND ETQLTQRALS
LLEENMFWAG VVFPDMYPWT SSLPPHVKYK IRMDIDVVEK TNKIKDRYWD SGPRADPVED
FRYIWGGFAY LQDMVEQGIT RSQVQAEAPV GIYLQQMPYP CFVDDSFMII LNRCFPIFMV
LAWIYSVSMT VKSIVLEKEL RLKETLKNQG VSNAVIWCTW FLDSFSIMSM SIFLLTIFIM
HGRILHYSDP FILFLFLLAF STATIMLCFL LSTFFSKASL AAACSGVIYF TLYLPHILCF
AWQDRMTAEL KKAVSLLSPV AFGFGTEYLV RFEEQGLGLQ WSNIGNSPTE GDEFSFLLSM
QMMLLDAAVY GLLAWYLDQV FPGDYGTPLP WYFLLQESYW LGGEGCSTRE ERALEKTEPL
TEETEDPEHP EGIHDSFFER EHPGWVPGVC VKNLVKIFEP CGRPAVDRLN ITFYENQITA
FLGHNGAGKT TTLSILTGLL PPTSGTVLVG GRDIETSLDA VRQSLGMCPQ HNILFHHLTV
AEHMLFYAQL KGKSQEEAQL EMEAMLEDTG LHHKRNEEAQ DLSGGMQRKL SVAIAFVGDA
KVVILDEPTS GVDPYSRRSI WDLLLKYRSG RTIIMSTHHM DEADLLGDRI AIIAQGRLYC
SGTPLFLKNC FGTGLYLTLV RKMKNIQSQR KGSEGTCSCS SKGFSTTCPA HVDDLTPEQV
LDGDVNELMD VVLHHVPEAK LVECIGQELI FLLPNKNFKH RAYASLFREL EETLADLGLS
SFGISDTPLE EIFLKVTEDS DSGPLFAGGA QQKRENVNPR HPCLGPREKA GQTPQDSNVC
SPGAPAAHPE GQPPPEPECP GPQLNTGTQL VLQHVQALLV KRFQHTIRSH KDFLAQIVLP
ATFVFLALML SIVIPPFGEY PALTLHPWIY GQQYTFFSMD EPGSEQFTVL ADVLLNKPGF
GNRCLKEGWL PEYPCGNSTP WKTPSVSPNI TQLFQKQKWT QVNPSPSCRC STREKLTMLP
ECPEGAGGLP PPQRTQRSTE ILQDLTDRNI SDFLVKTYPA LIRSSLKSKF WVNEQRYGGI
SIGGKLPVVP ITGEALVGFL SDLGRIMNVS GGPITREASK EIPDFLKHLE TEDNIKVWFN
NKGWHALVSF LNVAHNAILR ASLPKDRSPE EYGITVISQP LNLTKEQLSE ITVLTTSVDA
VVAICVIFSM SFVPASFVLY LIQERVNKSK HLQFISGVSP TTYWVTNFLW DIMNYSVSAG
LVVGIFIGFQ KKAYTSPENL PALVALLLLY GWAVIPMMYP ASFLFDVPST AYVALSCANL
FIGINSSAIT FILELFENNR TLLRFNAVLR KLLIVFPHFC LGRGLIDLAL SQAVTDVYAR
FGEEHSANPF HWDLIGKNLF AMVVEGVVYF LLTLLVQRHF FLSQWIAEPT KEPIVDEDDD
VAEERQRIIT GGNKTDILRL HELTKIYPGT SSPAVDRLCV GVRPGECFGL LGVNGAGKTT
TFKMLTGDTT VTSGDATVAG KSILTNISEV HQNMGYCPQF DAIDELLTGR EHLYLYARLR
GVPAEEIEKV ANWSIKSLGL TVYADCLAGT YSGGNKRKLS TAIALIGCPP LVLLDEPTTG
MDPQARRMLW NVIVSIIREG RAVVLTSHSM EECEALCTRL AIMVKGAFRC MGTIQHLKSK
FGDGYIVTMK IKSPKDDLLP DLNPVEQFFQ GNFPGSVQRE RHYNMLQFQV SSSSLARIFQ
LLLSHKDSLL IEEYSVTQTT LDQVFVNFAK QQTESHDLPL HPRAAGASRQ AQD*
mutated AA sequence MGFVRQIQLL LWKNWTLRKR QKIRFVVELV WPLSLFLVLI WLRNANPLYS HHECHFPNKA
MPSAGMLPWL QGIFCNVNNP CFQSPTPGES PGIVSNYNNS ILARVYRDFQ ELLMNAPESQ
HLGRIWTELH ILSQFMDTLR THPERIAGRG IRIRDILKDE ETLTLFLIKN IGLSDSVVYL
LINSQVRPEQ FAHGVPDLAL KDIACSEALL ERFIIFSQRR GAKTVRYALC SLSQGTLQWI
EDTLYANVDF FKLFRVLPTL LDSRSQGINL RSWGGILSDM SPRIQEFIHR PSMQDLLWVT
RPLMQNGGPE TFTKLMGILS DLLCGYPEGG GSRVLSFNWY EDNNYKAFLG IDSTRKDPIY
SYDRRTTSFC NALIQSLESN PLTKIAWRAA KPLLMGKILY TPDSPAARRI LKNANSTFEE
LEHVRKLVKA WEEVGPQIWY FFDNSTQMNM IRDTLGNPTV KDFLNRQLGE EGITAEAILN
FLYKGPRESQ ADDMANFDWR DIFNITDRTL RLVNQYLECL VLDKFESYND ETQLTQRALS
LLEENMFWAG VVFPDMYPWT SSLPPHVKYK IRMDIDVVEK TNKIKDRYWD SGPRADPVED
FRYIWGGFAY LQDMVEQGIT RSQVQAEAPV GIYLQQMPYP CFVDDSFMII LNRCFPIFMV
LAWIYSVSMT VKSIVLEKEL RLKETLKNQG VSNAVIWCTW FLDSFSIMSM SIFLLTIFIM
HGRILHYSDP FILFLFLLAF STATIMLCFL LSTFFSKASL AAACSGVIYF TLYLPHILCF
AWQDRMTAEL KKAVSLLSPV AFGFGTEYLV RFEEQGLGLQ WSNIGNSPTE GDEFSFLLSM
QMMLLDAAVY GLLAWYLDQV FPGDYGTPLP WYFLLQESYW LGGEGCSTRE ERALEKTEPL
TEETEDPEHP EGIHDSFFER EHPGWVPGVC VKNLVKIFEP CGRPAVDRLN ITFYENQITA
FLGHNGAGKT TTLSILTGLL PPTSGTVLVG GRDIETSLDA VRQSLGMCPQ HNILFHHLTV
AEHMLFYAQL KGKSQKEAQL EMEAMLEDTG LHHKRNEEAQ DLSGGMQRKL SVAIAFVGDA
KVVILDEPTS GVDPYSRRSI WDLLLKYRSG RTIIMSTHHM DEADLLGDRI AIIAQGRLYC
SGTPLFLKNC FGTGLYLTLV RKMKNIQSQR KGSEGTCSCS SKGFSTTCPA HVDDLTPEQV
LDGDVNELMD VVLHHVPEAK LVECIGQELI FLLPNKNFKH RAYASLFREL EETLADLGLS
SFGISDTPLE EIFLKVTEDS DSGPLFAGGA QQKRENVNPR HPCLGPREKA GQTPQDSNVC
SPGAPAAHPE GQPPPEPECP GPQLNTGTQL VLQHVQALLV KRFQHTIRSH KDFLAQIVLP
ATFVFLALML SIVIPPFGEY PALTLHPWIY GQQYTFFSMD EPGSEQFTVL ADVLLNKPGF
GNRCLKEGWL PEYPCGNSTP WKTPSVSPNI TQLFQKQKWT QVNPSPSCRC STREKLTMLP
ECPEGAGGLP PPQRTQRSTE ILQDLTDRNI SDFLVKTYPA LIRSSLKSKF WVNEQRYGGI
SIGGKLPVVP ITGEALVGFL SDLGRIMNVS GGPITREASK EIPDFLKHLE TEDNIKVWFN
NKGWHALVSF LNVAHNAILR ASLPKDRSPE EYGITVISQP LNLTKEQLSE ITVLTTSVDA
VVAICVIFSM SFVPASFVLY LIQERVNKSK HLQFISGVSP TTYWVTNFLW DIMNYSVSAG
LVVGIFIGFQ KKAYTSPENL PALVALLLLY GWAVIPMMYP ASFLFDVPST AYVALSCANL
FIGINSSAIT FILELFENNR TLLRFNAVLR KLLIVFPHFC LGRGLIDLAL SQAVTDVYAR
FGEEHSANPF HWDLIGKNLF AMVVEGVVYF LLTLLVQRHF FLSQWIAEPT KEPIVDEDDD
VAEERQRIIT GGNKTDILRL HELTKIYPGT SSPAVDRLCV GVRPGECFGL LGVNGAGKTT
TFKMLTGDTT VTSGDATVAG KSILTNISEV HQNMGYCPQF DAIDELLTGR EHLYLYARLR
GVPAEEIEKV ANWSIKSLGL TVYADCLAGT YSGGNKRKLS TAIALIGCPP LVLLDEPTTG
MDPQARRMLW NVIVSIIREG RAVVLTSHSM EECEALCTRL AIMVKGAFRC MGTIQHLKSK
FGDGYIVTMK IKSPKDDLLP DLNPVEQFFQ GNFPGSVQRE RHYNMLQFQV SSSSLARIFQ
LLLSHKDSLL IEEYSVTQTT LDQVFVNFAK QQTESHDLPL HPRAAGASRQ AQD*
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

Problems