ClinVar Miner

Submissions for variant NM_000275.3(OCA2):c.157del (p.Arg53fs)

gnomAD frequency: 0.00003  dbSNP: rs758894409
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001382526 SCV001581350 pathogenic not provided 2024-07-08 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg53Glyfs*49) in the OCA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in OCA2 are known to be pathogenic (PMID: 19865097, 21541274). This variant is present in population databases (rs758894409, gnomAD 0.004%). This premature translational stop signal has been observed in individual(s) with albinism (PMID: 27734839). ClinVar contains an entry for this variant (Variation ID: 1070405). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001382526 SCV001826964 pathogenic not provided 2021-02-19 criteria provided, single submitter clinical testing Identified in the heterozygous state in several individuals with oculocutaneous albinism, but a second OCA2 variant was not identified in these individuals (Gronskov et al., 2009; Urtatiz et al., 2014; Gao et al., 2017); Frameshift 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 (Lek et al., 2016); This variant is associated with the following publications: (PMID: 25455140, 19060277, 28451379)
Genome-Nilou Lab RCV001797836 SCV002040631 pathogenic Tyrosinase-positive oculocutaneous albinism 2021-11-07 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV001797836 SCV002581050 likely pathogenic Tyrosinase-positive oculocutaneous albinism 2022-07-12 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002499794 SCV002810509 pathogenic Tyrosinase-positive oculocutaneous albinism; SKIN/HAIR/EYE PIGMENTATION 1, BLUE/NONBLUE EYES 2024-05-15 criteria provided, single submitter clinical testing
Baylor Genetics RCV003462985 SCV004208999 pathogenic SKIN/HAIR/EYE PIGMENTATION 1, BLUE/NONBLUE EYES 2023-12-04 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004743448 SCV005367535 pathogenic OCA2-related disorder 2024-05-26 no assertion criteria provided clinical testing The OCA2 c.157delA variant is predicted to result in a frameshift and premature protein termination (p.Arg53Glyfs*49). This variant has been reported in the compound heterozygous state in individuals with oculocutaneous albinism (Mauri et al. 2016. PubMed ID: 27734839; Table S1, Wei et al. 2022. PubMed ID: 34838614). This variant is reported in 0.0027% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Frameshift variants in OCA2 are expected to be pathogenic. Given the evidence, we interpret this variant as pathogenic.

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