ClinVar Genomic variation as it relates to human health
NM_000350.3(ABCA4):c.2041C>T (p.Arg681Ter)
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000350.3(ABCA4):c.2041C>T (p.Arg681Ter)
Variation ID: 99114 Accession: VCV000099114.56
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1p22.1 1: 94060656 (GRCh38) [ NCBI UCSC ] 1: 94526212 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Feb 20, 2014 Jun 22, 2025 Nov 19, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000350.3:c.2041C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000341.2:p.Arg681Ter nonsense NM_001425324.1:c.2041C>T NP_001412253.1:p.Arg681Ter nonsense NC_000001.11:g.94060656G>A NC_000001.10:g.94526212G>A NG_009073.1:g.65494C>T NG_009073.2:g.65492C>T - Protein change
- R681*
- Other names
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- Canonical SPDI
- NC_000001.11:94060655:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00020 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00002
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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ABCA4 | - | - |
GRCh38 GRCh37 |
4050 | 4431 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (8) |
criteria provided, multiple submitters, no conflicts
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Nov 19, 2024 | RCV000085458.47 | |
Likely pathogenic (1) |
no assertion criteria provided
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Jan 19, 2015 | RCV000210310.3 | |
Pathogenic/Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 30, 2021 | RCV000408512.4 | |
Pathogenic (1) |
no assertion criteria provided
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Jan 1, 2015 | RCV000504983.3 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 1, 2022 | RCV001073628.4 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 21, 2019 | RCV001195987.4 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 27, 2024 | RCV005025147.1 | |
Pathogenic (1) |
no assertion criteria provided
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Sep 11, 2024 | RCV004732663.1 | |
Pathogenic (1) |
no assertion criteria provided
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- | RCV004558307.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Jan 01, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
|
Severe early-childhood-onset retinal dystrophy
Affected status: yes
Allele origin:
germline
|
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
Accession: SCV000281841.2
First in ClinVar: Dec 07, 2016 Last updated: Dec 07, 2016 |
Indication for testing: Stargardt disease 1
Zygosity: Single Heterozygote
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Pathogenic
(Jul 20, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
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Retinal dystrophy
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV001239179.1
First in ClinVar: Apr 18, 2020 Last updated: Apr 18, 2020
Comment:
My Retina Tracker patient
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Pathogenic
(Aug 21, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
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Age related macular degeneration 2
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001366414.2
First in ClinVar: Jul 04, 2020 Last updated: Dec 12, 2020 |
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP3,PP5.
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Pathogenic
(Apr 25, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000490370.4
First in ClinVar: Feb 20, 2014 Last updated: Mar 04, 2023 |
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 25544989, 28041643, 28118664, 26872967, 24342785, 24713488, 14517951, 10090887, 29555955, 29925512, 29736279, 28559085, 19074458) (less)
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Pathogenic
(Nov 09, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003812951.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 01, 2022)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Retinal dystrophy
Affected status: yes
Allele origin:
germline
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Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
Accession: SCV005073414.1
First in ClinVar: Dec 28, 2024 Last updated: Dec 28, 2024 |
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Pathogenic
(Mar 27, 2024)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Age related macular degeneration 2
Severe early-childhood-onset retinal dystrophy Retinitis pigmentosa 19 Cone-rod dystrophy 3
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Fulgent Genetics, Fulgent Genetics
Accession: SCV005661350.1
First in ClinVar: Jan 25, 2025 Last updated: Jan 25, 2025 |
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Pathogenic
(Jun 17, 2021)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001761996.2
First in ClinVar: Jul 30, 2021 Last updated: Apr 13, 2025 |
Clinical Features:
Cone-rod dystrophy (present)
Sex: male
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Pathogenic
(Jul 01, 2020)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001245781.31
First in ClinVar: May 09, 2020 Last updated: Jun 22, 2025 |
Number of individuals with the variant: 3
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Likely pathogenic
(Jan 30, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
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Severe early-childhood-onset retinal dystrophy
Affected status: yes
Allele origin:
germline
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Institute of Medical Molecular Genetics, University of Zurich
Accession: SCV001548009.1
First in ClinVar: Mar 28, 2021 Last updated: Mar 28, 2021 |
Test name: long-range PCR
Platform type: next-gen sequencing
Platform name: MiSeq
Method: long-range PCR
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Pathogenic
(Nov 19, 2024)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001393043.6
First in ClinVar: Jul 16, 2020 Last updated: Feb 25, 2025 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg681*) in the ABCA4 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg681*) in the ABCA4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABCA4 are known to be pathogenic (PMID: 10958761, 24938718, 25312043, 26780318). This variant is present in population databases (rs61749423, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with retinal disease (PMID: 10090887, 25544989, 28041643, 28559085). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 99114). For these reasons, this variant has been classified as Pathogenic. (less)
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Likely pathogenic
(Jan 19, 2015)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: clinical testing
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Bull's eye maculopathy
Affected status: yes
Allele origin:
germline
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Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals
Accession: SCV000259074.1
First in ClinVar: Mar 25, 2016 Last updated: Mar 25, 2016 |
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Pathogenic
(-)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001922875.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Pathogenic
(-)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: research
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Stargardt disease 3
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
|
Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana
Accession: SCV005046941.1
First in ClinVar: Jun 09, 2024 Last updated: Jun 09, 2024 |
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Pathogenic
(Jan 01, 2015)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: research
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Leber congenital amaurosis
Affected status: yes
Allele origin:
unknown
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NIHR Bioresource Rare Diseases, University of Cambridge
Accession: SCV000598948.2
First in ClinVar: Sep 09, 2017 Last updated: Apr 13, 2025 |
Number of individuals with the variant: 1
Sex: male
Ethnicity/Population group: NA
Platform type: Whole Exome Sequencing
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Pathogenic
(-)
N
Not contributing to aggregate classification
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001954765.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(Sep 11, 2024)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: clinical testing
|
ABCA4-related condition
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV005360403.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
The ABCA4 c.2041C>T variant is predicted to result in premature protein termination (p.Arg681*). This variant has been reported in multiple individuals with ABCA4-associated disease (see … (more)
The ABCA4 c.2041C>T variant is predicted to result in premature protein termination (p.Arg681*). This variant has been reported in multiple individuals with ABCA4-associated disease (see for example, Maugeri et al. 1999. PubMed ID: 10090887; Chouchene et al. 2013. PubMed ID: 24342785; Table S2, Del Pozo-Valero et al. 2020. PubMed ID: 32619608; Briggs et al. 2001. PubMed ID: 11527935; Supplementary tables, Holtan et al. 2020. PubMed ID: 31429209; Table S1, Schlottmann et al. 2023. PubMed ID: 37217489; Table S2, Carss et al. 2016. PubMed ID: 28041643). Nonsense variants in ABCA4 are expected to be pathogenic. This variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD. This variant is interpreted as pathogenic. (less)
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not provided
(-)
N
Not contributing to aggregate classification
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no classification provided
Method: not provided
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not provided
Affected status: not provided
Allele origin:
not provided
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Retina International
Accession: SCV000117595.1
First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_ABCR:c.2041C>T
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Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis. | Panneman DM | Frontiers in cell and developmental biology | 2023 | PMID: 36819107 |
Genetic epidemiology of inherited retinal diseases in a large patient cohort followed at a single center in Italy. | Karali M | Scientific reports | 2022 | PMID: 36460718 |
Impact of Next Generation Sequencing in Unraveling the Genetics of 1036 Spanish Families With Inherited Macular Dystrophies. | Del Pozo-Valero M | Investigative ophthalmology & visual science | 2022 | PMID: 35119454 |
Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases. | Maggi J | International journal of molecular sciences | 2021 | PMID: 33546218 |
Genotype-Phenotype Correlations in a Spanish Cohort of 506 Families With Biallelic ABCA4 Pathogenic Variants. | Del Pozo-Valero M | American journal of ophthalmology | 2020 | PMID: 32619608 |
Genetic architecture of inherited retinal degeneration in Germany: A large cohort study from a single diagnostic center over a 9-year period. | Weisschuh N | Human mutation | 2020 | PMID: 32531858 |
Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics. | Khan M | Genetics in medicine : official journal of the American College of Medical Genetics | 2020 | PMID: 32307445 |
Expanding the Clinical and Molecular Heterogeneity of Nonsyndromic Inherited Retinal Dystrophies. | Rodríguez-Muñoz A | The Journal of molecular diagnostics : JMD | 2020 | PMID: 32036094 |
Worldwide carrier frequency and genetic prevalence of autosomal recessive inherited retinal diseases. | Hanany M | Proceedings of the National Academy of Sciences of the United States of America | 2020 | PMID: 31964843 |
Inherited retinal disease in Norway - a characterization of current clinical and genetic knowledge. | Holtan JP | Acta ophthalmologica | 2020 | PMID: 31429209 |
Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes. | Capalbo A | PLoS genetics | 2019 | PMID: 31589614 |
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 |
Phenotypic Progression of Stargardt Disease in a Large Consanguineous Tunisian Family Harboring New ABCA4 Mutations. | Falfoul Y | Journal of ophthalmology | 2018 | PMID: 29736279 |
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 |
Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease. | Carss KJ | American journal of human genetics | 2017 | PMID: 28041643 |
Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease. | Ellingford JM | Ophthalmology | 2016 | PMID: 26872967 |
Screening of ABCA4 Gene in a Chinese Cohort With Stargardt Disease or Cone-Rod Dystrophy With a Report on 85 Novel Mutations. | Jiang F | Investigative ophthalmology & visual science | 2016 | PMID: 26780318 |
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. | Xiong HY | Science (New York, N.Y.) | 2015 | PMID: 25525159 |
Clinical and molecular characteristics of childhood-onset Stargardt disease. | Fujinami K | Ophthalmology | 2015 | PMID: 25312043 |
Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. | González-del Pozo M | PloS one | 2014 | PMID: 25544989 |
Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing. | Xu Y | Human genetics | 2014 | PMID: 24938718 |
Generalized choriocapillaris dystrophy, a distinct phenotype in the spectrum of ABCA4-associated retinopathies. | Bertelsen M | Investigative ophthalmology & visual science | 2014 | PMID: 24713488 |
[Clinical characterization of the Stargardt disease and molecular exploration of the c.2041C>T mutation (ABCA4 gene) in Tunisian patients]. | Chouchene I | Annales de biologie clinique | 2013 | PMID: 24342785 |
ABCA4 disease progression and a proposed strategy for gene therapy. | Cideciyan AV | Human molecular genetics | 2009 | PMID: 19074458 |
Mutations in the ABCA4 (ABCR) gene are the major cause of autosomal recessive cone-rod dystrophy. | Maugeri A | American journal of human genetics | 2000 | PMID: 10958761 |
The 2588G-->C mutation in the ABCR gene is a mild frequent founder mutation in the Western European population and allows the classification of ABCR mutations in patients with Stargardt disease. | Maugeri A | American journal of human genetics | 1999 | PMID: 10090887 |
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Text-mined citations for rs61749423 ...
HelpRecord last updated Jun 22, 2025
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.