Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999374038242 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983377)
  • known disease mutation: rs7893 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:94473283A>CN/A show variant in all transcripts   IGV
HGNC symbol ABCA4
Ensembl transcript ID ENST00000535881
Genbank transcript ID N/A
UniProt peptide P78363
alteration type single base exchange
alteration region CDS
DNA changes c.269T>G
cDNA.494T>G
g.113406T>G
AA changes L90R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 90
frameshift no
known variant Reference ID: rs61753034
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs7893 (pathogenic for Stargardt disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983377)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983377)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983377)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3481
4.9071
(flanking)1.7150.999
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 increased113407wt: 0.7507 / mu: 0.7562 (marginal change - not scored)wt: TCCTAGTGCTTTGGCCTCCTGGGAGTGAATGGTGCCGGCAA
mu: TCCTAGTGCTTTGGCCTCCGGGGAGTGAATGGTGCCGGCAA		 cctg|GGAG
Acc increased113398wt: 0.60 / mu: 0.75wt: TGTGTTTTCTCCTAGTGCTTTGGCCTCCTGGGAGTGAATGG
mu: TGTGTTTTCTCCTAGTGCTTTGGCCTCCGGGGAGTGAATGG		 cttt|GGCC
Acc marginally increased113399wt: 0.9274 / mu: 0.9430 (marginal change - not scored)wt: GTGTTTTCTCCTAGTGCTTTGGCCTCCTGGGAGTGAATGGT
mu: GTGTTTTCTCCTAGTGCTTTGGCCTCCGGGGAGTGAATGGT		 tttg|GCCT
Acc increased113400wt: 0.68 / mu: 0.77wt: TGTTTTCTCCTAGTGCTTTGGCCTCCTGGGAGTGAATGGTG
mu: TGTTTTCTCCTAGTGCTTTGGCCTCCGGGGAGTGAATGGTG		 ttgg|CCTC
Donor marginally increased113410wt: 0.8184 / mu: 0.8220 (marginal change - not scored)wt: CTGGGAGTGAATGGT
mu: CGGGGAGTGAATGGT		 GGGA|gtga
Donor increased113405wt: 0.56 / mu: 0.97wt: GCCTCCTGGGAGTGA
mu: GCCTCCGGGGAGTGA		 CTCC|tggg
Acc gained1134050.64mu: TCTCCTAGTGCTTTGGCCTCCGGGGAGTGAATGGTGCCGGC ctcc|GGGG
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      90VGVRPGECFGLLGVNGAGKTTTFK
mutated  not conserved    90VGVRPGECFGLRGVNGAGKTTTF
Ptroglodytes  all identical  ENSPTRG00000023377  1971VGVRPGECFGLLGVNGAGKTTTF
Mmulatta  all identical  ENSMMUG00000013858  962ITFYENQITAFLGHNGAGKTTTL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028125  1970VGVRPGECFGLLGVNGAGKTTTF
Ggallus  all identical  ENSGALG00000005752  1965VGIRPGECFGLLGVNGAGKTTTF
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000062661  2036VGVPAGECFGLLGVNGAGKTTTF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008223  2046VGVRPGECFGLLGVNGAGKTTTF
protein features
start (aa)end (aa)featuredetails 
43646TOPO_DOMExtracellular.lost
9898CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
324324DISULFIDBy similarity.might get lost (downstream of altered splice site)
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 1179 / 1179
position (AA) of stopcodon in wt / mu AA sequence 393 / 393
position of stopcodon in wt / mu cDNA 1404 / 1404
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 226 / 226
chromosome 1
strand -1
last intron/exon boundary 1399
theoretical NMD boundary in CDS 1123
length of CDS 1179
coding sequence (CDS) position 269
cDNA position
(for ins/del: last normal base / first normal base)		 494
gDNA position
(for ins/del: last normal base / first normal base)		 113406
chromosomal position
(for ins/del: last normal base / first normal base)		 94473283
original gDNA sequence snippet CTCCTAGTGCTTTGGCCTCCTGGGAGTGAATGGTGCCGGCA
altered gDNA sequence snippet CTCCTAGTGCTTTGGCCTCCGGGGAGTGAATGGTGCCGGCA
original cDNA sequence snippet TGGAGAGTGCTTTGGCCTCCTGGGAGTGAATGGTGCCGGCA
altered cDNA sequence snippet TGGAGAGTGCTTTGGCCTCCGGGGAGTGAATGGTGCCGGCA
wildtype AA sequence MVVEGVVYFL LTLLVQRHFF LSQWIAEPTK EPIVDEDDDV AEERQRIITG GNKTDILRLH
ELTKIYPGTS SPAVDRLCVG VRPGECFGLL GVNGAGKTTT FKMLTGDTTV TSGDATVAGK
SILTNISEVH QNMGYCPQFD AIDELLTGRE HLYLYARLRG VPAEEIEKVA NWSIKSLGLT
VYADCLAGTY SGGNKRKLST AIALIGCPPL VLLDEPTTGM DPQARRMLWN VIVSIIREGR
AVVLTSHSME ECEALCTRLA IMVKGAFRCM GTIQHLKSKF GDGYIVTMKI KSPKDDLLPD
LNPVEQFFQG NFPGSVQRER HYNMLQFQVS SSSLARIFQL LLSHKDSLLI EEYSVTQTTL
DQVFVNFAKQ QTESHDLPLH PRAAGASRQA QD*
mutated AA sequence MVVEGVVYFL LTLLVQRHFF LSQWIAEPTK EPIVDEDDDV AEERQRIITG GNKTDILRLH
ELTKIYPGTS SPAVDRLCVG VRPGECFGLR GVNGAGKTTT FKMLTGDTTV TSGDATVAGK
SILTNISEVH QNMGYCPQFD AIDELLTGRE HLYLYARLRG VPAEEIEKVA NWSIKSLGLT
VYADCLAGTY SGGNKRKLST AIALIGCPPL VLLDEPTTGM DPQARRMLWN VIVSIIREGR
AVVLTSHSME ECEALCTRLA IMVKGAFRCM GTIQHLKSKF GDGYIVTMKI KSPKDDLLPD
LNPVEQFFQG NFPGSVQRER HYNMLQFQVS SSSLARIFQL LLSHKDSLLI EEYSVTQTTL
DQVFVNFAKQ QTESHDLPLH PRAAGASRQA QD*
speed 1.05 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