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 ENST00000536513
Genbank transcript ID N/A
UniProt peptide P78363
alteration type single base exchange
alteration region CDS
DNA changes c.889C>T
cDNA.982C>T
g.115624C>T
AA changes L297F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 297
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      297YCPQFDAIDELLTGREHLYLYARL
mutated  not conserved    297YCPQFDAIDELFTGR
Ptroglodytes  all identical  ENSPTRG00000023377  2027YCPQFDAIDELLTGRE
Mmulatta  all identical  ENSMMUG00000013858  1018MCPQHNILFHHLTVAEHILFYAQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028125  2026YCPQFDAIDDLLTGRE
Ggallus  all identical  ENSGALG00000005752  2021YCPQFDALDDLLTGRE
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000062661  2092YCPQFDAIDELLTGRE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008223  2102YCPQFDAIDDLLTGRE
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 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 889
cDNA position
(for ins/del: last normal base / first normal base)		 982
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 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 GGNKTDILRL HELTKIYPGT SSPAVDRLCV GVRPGECFGL
LGVNGAGKTT TFKMLTGDTT VTSGDATVAG KSILTNISEV HQNMGYCPQF DAIDELFTGR
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 1.36 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