Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999740597172 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970018)
  • known disease mutation: rs7882 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:94471065G>AN/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.436C>T
cDNA.661C>T
g.115624C>T
AA changes L146F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS
146
frameshift no
known variant Reference ID: rs61751408
databasehomozygous (A/A)heterozygousallele carriers
1000G011
ExAC02626

known disease mutation: rs7882 (pathogenic for Retinal dystrophy|Age-related macular degeneration 2|Stargardt disease 1|Retinitis pigmentosa 19|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 CM970018)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970018)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2051
4.6041
(flanking)1.3411
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      146YCPQFDAIDELLTGREHLYLYARL
mutated  not conserved    146YCPQFDAIDELFTGREHLYLYAR
Ptroglodytes  all identical  ENSPTRG00000023377  2027YCPQFDAIDELLTGREHLYLYAR
Mmulatta  all identical  ENSMMUG00000013858  1018MCPQHNILFHHLTVAEHILFYAQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028125  2026YCPQFDAIDDLLTGREHLYLYAR
Ggallus  all identical  ENSGALG00000005752  2021YCPQFDALDDLLTGREHLYLYAR
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000062661  2092YCPQFDAIDELLTGREHLYLYAR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008223  2102YCPQFDAIDDLLTGREHLQLYGR
protein features
start (aa)end (aa)featuredetails 
43646TOPO_DOMExtracellular.lost
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 436
cDNA position
(for ins/del: last normal base / first normal base)
661
gDNA position
(for ins/del: last normal base / first normal base)
115624
chromosomal position
(for ins/del: last normal base / first normal base)
94471065
original gDNA sequence snippet TTGATGCAATTGATGAGCTGCTCACAGGACGAGAACATCTT
altered gDNA sequence snippet TTGATGCAATTGATGAGCTGTTCACAGGACGAGAACATCTT
original cDNA sequence snippet TTGATGCAATTGATGAGCTGCTCACAGGACGAGAACATCTT
altered cDNA sequence snippet TTGATGCAATTGATGAGCTGTTCACAGGACGAGAACATCTT
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 VRPGECFGLL GVNGAGKTTT FKMLTGDTTV TSGDATVAGK
SILTNISEVH QNMGYCPQFD AIDELFTGRE 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 1.17 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