Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999924745278 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM175549)
  • known disease mutation at this position (HGMD CM990020)
  • known disease mutation: rs7896 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:94546115A>CN/A show variant in all transcripts   IGV
HGNC symbol ABCA4
Ensembl transcript ID ENST00000535735
Genbank transcript ID N/A
UniProt peptide P78363
alteration type single base exchange
alteration region CDS
DNA changes c.1018T>G
cDNA.1098T>G
g.40574T>G
AA changes Y340D Score: 160 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 340
frameshift no
known variant Reference ID: rs61748548
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs7896 (pathogenic for Stargardt disease 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM175549)

known disease mutation at this position, please check HGMD for details (HGMD ID CM175549)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990020)

known disease mutation at this position, please check HGMD for details (HGMD ID CM175549)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990020)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990020)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.571
4.571
(flanking)5.2881
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased40568wt: 0.9320 / mu: 0.9483 (marginal change - not scored)wt: GCTCTCGGGTGCTCTCCTTCAACTGGTATGAAGACAATAAC
mu: GCTCTCGGGTGCTCTCCTTCAACTGGGATGAAGACAATAAC		 ttca|ACTG
Acc marginally increased40564wt: 0.5522 / mu: 0.5588 (marginal change - not scored)wt: GGTGGCTCTCGGGTGCTCTCCTTCAACTGGTATGAAGACAA
mu: GGTGGCTCTCGGGTGCTCTCCTTCAACTGGGATGAAGACAA		 ctcc|TTCA
Acc increased40567wt: 0.44 / mu: 0.58wt: GGCTCTCGGGTGCTCTCCTTCAACTGGTATGAAGACAATAA
mu: GGCTCTCGGGTGCTCTCCTTCAACTGGGATGAAGACAATAA		 cttc|AACT
Acc marginally increased40571wt: 0.4879 / mu: 0.4952 (marginal change - not scored)wt: CTCGGGTGCTCTCCTTCAACTGGTATGAAGACAATAACTAT
mu: CTCGGGTGCTCTCCTTCAACTGGGATGAAGACAATAACTAT		 aact|GGTA
Acc marginally increased40569wt: 0.8094 / mu: 0.8334 (marginal change - not scored)wt: CTCTCGGGTGCTCTCCTTCAACTGGTATGAAGACAATAACT
mu: CTCTCGGGTGCTCTCCTTCAACTGGGATGAAGACAATAACT		 tcaa|CTGG
Donor marginally increased40579wt: 0.9161 / mu: 0.9724 (marginal change - not scored)wt: TATGAAGACAATAAC
mu: GATGAAGACAATAAC		 TGAA|gaca
Donor marginally increased40574wt: 0.7948 / mu: 0.8617 (marginal change - not scored)wt: ACTGGTATGAAGACA
mu: ACTGGGATGAAGACA		 TGGT|atga
Donor increased40571wt: 0.83 / mu: 0.93wt: TCAACTGGTATGAAG
mu: TCAACTGGGATGAAG		 AACT|ggta
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      340GGGSRVLSFNWYEDNNYKAFLGID
mutated  not conserved    340GGGSRVLSFNWDEDNNYKAFLGI
Ptroglodytes  all identical  ENSPTRG00000023377  340GGGSRVLSFNWYEDNNYKAFLGI
Mmulatta  all identical  ENSMMUG00000013858  340GGGSRVLSFNWYEDNNYKAFLGI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028125  340GGGSRVFSFNWYEDNNYKAFLGI
Ggallus  all identical  ENSGALG00000005752  340GGGSRVLSFNWYEDNNYKAFLGI
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000062661  340GEGTRVFSFNWYEDNNYKAFLGI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008223  340GGGARVFSFNWYEDNNYKVFLGV
protein features
start (aa)end (aa)featuredetails 
43646TOPO_DOMExtracellular.lost
415415CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
444444CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
504504CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
647667TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
700720TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
722722CONFLICTG -> V (in Ref. 2; AAC23915).might get lost (downstream of altered splice site)
731751TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
760780TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
836856TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
849849CONFLICTV -> C (in Ref. 1; AAC51144).might get lost (downstream of altered splice site)
8571376TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
882882CONFLICTG -> S (in Ref. 1; AAC51144 and 3; CAA75729).might get lost (downstream of altered splice site)
9291160DOMAINABC transporter 1.might get lost (downstream of altered splice site)
941941CONFLICTC -> S (in Ref. 2; AAC23915).might get lost (downstream of altered splice site)
963970NP_BINDATP 1 (Potential).might get lost (downstream of altered splice site)
966966MUTAGENG->D: Abolishes basal and retinal- stimulated ATP hydrolysis.might get lost (downstream of altered splice site)
969969MUTAGENK->M: Abolishes basal and retinal- stimulated ATP hydrolysis.might get lost (downstream of altered splice site)
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 2940 / 2940
position (AA) of stopcodon in wt / mu AA sequence 980 / 980
position of stopcodon in wt / mu cDNA 3020 / 3020
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 81 / 81
chromosome 1
strand -1
last intron/exon boundary 2777
theoretical NMD boundary in CDS 2646
length of CDS 2940
coding sequence (CDS) position 1018
cDNA position
(for ins/del: last normal base / first normal base)		 1098
gDNA position
(for ins/del: last normal base / first normal base)		 40574
chromosomal position
(for ins/del: last normal base / first normal base)		 94546115
original gDNA sequence snippet GGGTGCTCTCCTTCAACTGGTATGAAGACAATAACTATAAG
altered gDNA sequence snippet GGGTGCTCTCCTTCAACTGGGATGAAGACAATAACTATAAG
original cDNA sequence snippet GGGTGCTCTCCTTCAACTGGTATGAAGACAATAACTATAAG
altered cDNA sequence snippet GGGTGCTCTCCTTCAACTGGGATGAAGACAATAACTATAAG
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
SLLSPVAFGF GTEYLVRFEE QGLGLQWSNI GNSPTEGDEF SFLLSMQMML LDAAVYGLLA
WYLDQVFPGD YGTPLPWYFL LQESYWLGGE GCSTREERAL EKTEPLTEET EDPEHPEGIH
DSFFEREHPG WVPGVCVKNL VKIFEPCGRP AVDRLNITFY ENQITAFLGH NGAGKTTTFS
AGAPLSSKGP ERHLLRGEHG PPWFPKEQQT RTSQGAANPR DTVFKSFGEP QEGTTACTPC
DGMFSRAVQC EWNVGPVPF*
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 GSRVLSFNWD 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
SLLSPVAFGF GTEYLVRFEE QGLGLQWSNI GNSPTEGDEF SFLLSMQMML LDAAVYGLLA
WYLDQVFPGD YGTPLPWYFL LQESYWLGGE GCSTREERAL EKTEPLTEET EDPEHPEGIH
DSFFEREHPG WVPGVCVKNL VKIFEPCGRP AVDRLNITFY ENQITAFLGH NGAGKTTTFS
AGAPLSSKGP ERHLLRGEHG PPWFPKEQQT RTSQGAANPR DTVFKSFGEP QEGTTACTPC
DGMFSRAVQC EWNVGPVPF*
speed 0.57 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