Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.619659215837977 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM011908)
  • known disease mutation: rs7911 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:94474323A>GN/A show variant in all transcripts   IGV
HGNC symbol ABCA4
Ensembl transcript ID ENST00000536513
Genbank transcript ID N/A
UniProt peptide P78363
alteration type single base exchange
alteration region CDS
DNA changes c.629T>C
cDNA.722T>C
g.112366T>C
AA changes L210P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 210
frameshift no
known variant Reference ID: rs61753033
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs7911 (pathogenic for Stargardt disease 1|Cone-rod dystrophy 3|Stargardt disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011908)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011908)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011908)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0660.096
3.0830.134
(flanking)0.5570.053
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased112357wt: 0.9735 / mu: 0.9845 (marginal change - not scored)wt: TGACATCTTAAGGCT
mu: TGACATCTTAAGGCC		 ACAT|ctta
Donor increased112368wt: 0.38 / mu: 0.50wt: GGCTACATGAACTAA
mu: GGCCACATGAACTAA		 CTAC|atga
Donor increased112363wt: 0.83 / mu: 0.92wt: CTTAAGGCTACATGA
mu: CTTAAGGCCACATGA		 TAAG|gcta
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      210ITGGNKTDILRLHELTKIYPGTSS
mutated  not conserved    210ITGGNKTDILRPHELTKIYPGTS
Ptroglodytes  all identical  ENSPTRG00000023377  1940ITGGNKTDILRLHELTKIYPGTS
Mmulatta  no alignment  ENSMMUG00000013858  n/a
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028125  1939MSGGNKTDILKLNELTKVYSGSS
Ggallus  all identical  ENSGALG00000005752  1934LNGGNKTNILELQELTKIYAGRH
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000062661  2005YKGGNKNDILLIRDLSKTYRRRK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008223  2015IKGGGKNDILKLKELTKTYPGKQ
protein features
start (aa)end (aa)featuredetails 
43646TOPO_DOMExtracellular.lost
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 1632 / 1632
position (AA) of stopcodon in wt / mu AA sequence 544 / 544
position of stopcodon in wt / mu cDNA 1725 / 1725
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 94 / 94
chromosome 1
strand -1
last intron/exon boundary 1720
theoretical NMD boundary in CDS 1576
length of CDS 1632
coding sequence (CDS) position 629
cDNA position
(for ins/del: last normal base / first normal base)		 722
gDNA position
(for ins/del: last normal base / first normal base)		 112366
chromosomal position
(for ins/del: last normal base / first normal base)		 94474323
original gDNA sequence snippet TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGGTAA
altered gDNA sequence snippet TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGGTAA
original cDNA sequence snippet TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGATTT
altered cDNA sequence snippet TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGATTT
wildtype AA sequence MMMNYSVSAG 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 MMMNYSVSAG LVVGIFIGFQ KKAYTSPENL PALVALLLLY GWAVIPMMYP ASFLFDVPST
AYVALSCANL FIGINSSAIT FILELFENNR TLLRFNAVLR KLLIVFPHFC LGRGLIDLAL
SQAVTDVYAR FGEEHSANPF HWDLIGKNLF AMVVEGVVYF LLTLLVQRHF FLSQWIAEPT
KEPIVDEDDD VAEERQRIIT GGNKTDILRP 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 0.86 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