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NM_000350.3(ABCA4):c.4462T>C (p.Cys1488Arg)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 15, 2021)
Last evaluated:
Sep 15, 2021
Accession:
VCV000099284.14
Variation ID:
99284
Description:
single nucleotide variant
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NM_000350.3(ABCA4):c.4462T>C (p.Cys1488Arg)

Allele ID
105173
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p22.1
Genomic location
1: 94029522 (GRCh38) GRCh38 UCSC
1: 94495078 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P78363:p.Cys1488Arg
NC_000001.10:g.94495078A>G
NC_000001.11:g.94029522A>G
... more HGVS
Protein change
C1488R
Other names
-
Canonical SPDI
NC_000001.11:94029521:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA227193
UniProtKB: P78363#VAR_008453
dbSNP: rs61750146
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts Sep 15, 2021 RCV000085637.8
Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jan 30, 2021 RCV000408472.3
Likely pathogenic 1 criteria provided, single submitter Oct 31, 2018 RCV000763043.1
Pathogenic 1 criteria provided, single submitter Jul 20, 2019 RCV001073630.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ABCA4 - - GRCh38
GRCh37
2111 2141

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jan 01, 2016)
criteria provided, single submitter
Method: clinical testing
Stargardt disease 1
Allele origin: germline
Institute of Human Genetics, Univ. Regensburg,Univ. Regensburg
Accession: SCV000281892.2
Submitted: (May 25, 2016)
Evidence details
Publications
PubMed (4)
Pathogenic
(Oct 12, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000321351.7
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The C1488R pathogenic variant in the ABCA4 gene has been published previously in association with Stargardt disease (Lewis et al., 1999; Briggs et al., 2001; … (more)
Likely pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Age-related macular degeneration 2
Stargardt disease 1
Retinitis pigmentosa 19
Cone-rod dystrophy 3
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893524.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Jul 20, 2019)
criteria provided, single submitter
Method: clinical testing
Retinal dystrophy
Allele origin: germline
Blueprint Genetics
Accession: SCV001239181.1
Submitted: (Oct 15, 2019)
Comment:
My Retina Tracker patient
Evidence details
Likely pathogenic
(Jan 30, 2021)
criteria provided, single submitter
Method: clinical testing
Stargardt disease 1
Allele origin: unknown
Institute of Medical Molecular Genetics, University of Zurich
Accession: SCV001548141.1
Submitted: (Mar 19, 2021)
Evidence details
Publications
PubMed (1)
Pathogenic
(Dec 14, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001222273.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change replaces cysteine with arginine at codon 1488 of the ABCA4 protein (p.Cys1488Arg). The cysteine residue is highly conserved and there is a … (more)
Likely pathogenic
(Sep 15, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
(Autosomal recessive inheritance)
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001905554.1
Submitted: (Sep 15, 2021)
Evidence details
Pathogenic
(Jun 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001248244.6
Submitted: (Jul 04, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
Retina International
Accession: SCV000117776.1
Submitted: (Dec 20, 2012)
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_ABCR:c.4462T>C
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases. Maggi J International journal of molecular sciences 2021 PMID: 33546218
Detailed genetic characteristics of an international large cohort of patients with Stargardt disease: ProgStar study report 8. Fujinami K The British journal of ophthalmology 2019 PMID: 29925512
Clinical and genetic characteristics of 251 consecutive patients with macular and cone/cone-rod dystrophy. Birtel J Scientific reports 2018 PMID: 29555955
Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. Stone EM Ophthalmology 2017 PMID: 28559085
Mutation Spectrum of the ABCA4 Gene in 335 Stargardt Disease Patients From a Multicenter German Cohort-Impact of Selected Deep Intronic Variants and Common SNPs. Schulz HL Investigative ophthalmology & visual science 2017 PMID: 28118664
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Generalized choriocapillaris dystrophy, a distinct phenotype in the spectrum of ABCA4-associated retinopathies. Bertelsen M Investigative ophthalmology & visual science 2014 PMID: 24713488
Clinical and genetic characteristics of late-onset Stargardt's disease. Westeneng-van Haaften SC Ophthalmology 2012 PMID: 22449572
Biochemical defects in ABCR protein variants associated with human retinopathies. Sun H Nature genetics 2000 PMID: 11017087
Genotype/Phenotype analysis of a photoreceptor-specific ATP-binding cassette transporter gene, ABCR, in Stargardt disease. Lewis RA American journal of human genetics 1999 PMID: 9973280

Text-mined citations for rs61750146...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021