chr1:94008251:C>T Detail (hg38) (ABCA4)

Information

Genome

Assembly Position
hg19 chr1:94,473,807-94,473,807 View the variant detail on this assembly version.
hg38 chr1:94,008,251-94,008,251

HGVS

Type Transcript Protein
RefSeq NM_000350.2:c.5882G>A NP_000341.2:p.Gly1961Glu
Ensemble ENST00000370225.4:c.5882G>A ENST00000370225.4:p.Gly1961Glu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic low penetrance
Review star
Show details
Links
Type Database ID Link
Gene MIM 601691 OMIM
HGNC 34 HGNC
Ensembl ENSG00000198691 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2420237 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2008-07-01 no assertion criteria provided MACULAR DEGENERATION, AGE-RELATED, 2, SUSCEPTIBILITY TO germline Detail
Pathogenic Likely pathogenic 2024-03-25 criteria provided, multiple submitters, no conflicts Severe early-childhood-onset retinal dystrophy germline maternal unknown Detail
Pathogenic 2021-04-14 criteria provided, multiple submitters, no conflicts cone-rod dystrophy 3 germline unknown Detail
Pathogenic Pathogenic low penetrance 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline not provided unknown Detail
Pathogenic 2024-01-18 criteria provided, multiple submitters, no conflicts ABCA4-related disorder germline Detail
Pathogenic 2021-11-22 criteria provided, single submitter unknown Detail
Pathogenic 2023-10-01 criteria provided, multiple submitters, no conflicts Retinal dystrophy germline unknown Detail
Pathogenic 2014-09-07 criteria provided, single submitter Inborn genetic diseases germline Detail
Pathogenic Likely pathogenic 2019-09-05 criteria provided, multiple submitters, no conflicts age related macular degeneration 2 germline inherited unknown Detail
Pathogenic 2017-12-13 no assertion criteria provided Stargardt disease inherited Detail
Pathogenic Likely pathogenic 2021-10-25 criteria provided, multiple submitters, no conflicts Stargardt disease germline inherited unknown Detail
Likely pathogenic 2019-06-20 criteria provided, single submitter Severe early-childhood-onset retinal dystrophy,cone-rod dystrophy 3,retinitis pigmentosa 19 germline Detail
Likely pathogenic 2019-06-20 criteria provided, single submitter Severe early-childhood-onset retinal dystrophy,cone-rod dystrophy 3,retinitis pigmentosa 19 germline Detail
Likely pathogenic 2019-06-20 criteria provided, single submitter Severe early-childhood-onset retinal dystrophy,cone-rod dystrophy 3,retinitis pigmentosa 19 germline Detail
Pathogenic criteria provided, single submitter retinitis pigmentosa 19 germline Detail
no classifications from unflagged records 2022-05-19 no classifications from unflagged records not specified germline Detail
Pathogenic 2019-04-23 criteria provided, single submitter cone-rod dystrophy germline Detail
Likely pathogenic criteria provided, single submitter retinitis pigmentosa germline Detail
Pathogenic 2023-08-29 criteria provided, single submitter ABCA4-related retinopathy unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.442 STARGARDT DISEASE 1 (disorder) NA CLINVAR Detail
0.440 CONE-ROD DYSTROPHY 3 (disorder) NA CLINVAR Detail
0.004 Disorder of macula of retina G1961E mutant allele in the Stargardt disease gene ABCA4 causes bull's eye macul... BeFree 19217903 Detail
0.442 STARGARDT DISEASE 1 (disorder) Twenty-nine patients with Stargardt dystrophy or fundus flavimaculatus from diff... UNIPROT 10206579 Detail
0.169 age related macular degeneration Associations of the G1961E and D2177N variants in ABCA4 and the risk of age-rela... BeFree 25921964 Detail
0.004 Macular dystrophy Three patients had a Gly1961Glu missense mutation, the most common variant in St... BeFree 18024811 Detail
0.169 age related macular degeneration Three patients had a Gly1961Glu missense mutation, the most common variant in St... BeFree 18024811 Detail
0.004 Hereditary macular dystrophy Three patients had a Gly1961Glu missense mutation, the most common variant in St... BeFree 18024811 Detail
<0.001 muscular dystrophy Three patients had a Gly1961Glu missense mutation, the most common variant in St... BeFree 18024811 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND MACULAR DEGENERATION, AGE-RELATED, 2, SUSCEPTIBILITY... ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Severe early-childhood-onset retinal dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Cone-rod dystrophy 3 ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND not provided ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND ABCA4-related disorder ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Macular dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Retinal dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Inborn genetic diseases ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Age related macular degeneration 2 ClinVar Detail
NM_000350.2(ABCA4):c.[5512C>G;5882G>A] AND Stargardt disease ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Stargardt disease ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND multiple conditions ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND multiple conditions ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND multiple conditions ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Retinitis pigmentosa 19 ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND not specified ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Cone-rod dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Retinitis pigmentosa ClinVar Detail
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND ABCA4-related retinopathy ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
G1961E mutant allele in the Stargardt disease gene ABCA4 causes bull's eye maculopathy. DisGeNET Detail
Twenty-nine patients with Stargardt dystrophy or fundus flavimaculatus from different pedigrees were... DisGeNET Detail
Associations of the G1961E and D2177N variants in ABCA4 and the risk of age-related macular degenera... DisGeNET Detail
Three patients had a Gly1961Glu missense mutation, the most common variant in Stargardt disease (STG... DisGeNET Detail
Three patients had a Gly1961Glu missense mutation, the most common variant in Stargardt disease (STG... DisGeNET Detail
Three patients had a Gly1961Glu missense mutation, the most common variant in Stargardt disease (STG... DisGeNET Detail
Three patients had a Gly1961Glu missense mutation, the most common variant in Stargardt disease (STG... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1800553 dbSNP
Genome
hg38
Position
chr1:94,008,251-94,008,251
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1800553
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0003
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.4674063800277393E-4
Chromosome Counts in All Race (ExAC)
121302
Allele Counts in All Race (ExAC)
613
Heterozygous Counts in All Race (ExAC)
605
Homozygous Counts in All Race (ExAC)
4
Allele Frequency in All Race (ExAC)
0.005053502827653295
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