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NM_000275.3(OCA2):c.1465A>G (p.Asn489Asp) AND Oculocutaneous albinism

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 12, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003492280.1

Allele description [Variation Report for NM_000275.3(OCA2):c.1465A>G (p.Asn489Asp)]

NM_000275.3(OCA2):c.1465A>G (p.Asn489Asp)

Gene:
OCA2:OCA2 melanosomal transmembrane protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q13.1
Genomic location:
Preferred name:
NM_000275.3(OCA2):c.1465A>G (p.Asn489Asp)
HGVS:
  • NC_000015.10:g.27983383T>C
  • NG_009846.1:g.120930A>G
  • NM_000275.3:c.1465A>GMANE SELECT
  • NM_001300984.2:c.1393A>G
  • NP_000266.2:p.Asn489Asp
  • NP_001287913.1:p.Asn465Asp
  • NC_000015.9:g.28228529T>C
  • NM_000275.2:c.1465A>G
  • Q04671:p.Asn489Asp
Protein change:
N465D; ASN489ASP
Links:
UniProtKB: Q04671#VAR_006135; OMIM: 611409.0010; dbSNP: rs121918170
NCBI 1000 Genomes Browser:
rs121918170
Molecular consequence:
  • NM_000275.3:c.1465A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001300984.2:c.1393A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Oculocutaneous albinism
Identifiers:
MONDO: MONDO:0018910; MedGen: C0078918; OMIM: PS203100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004240913Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Dec 12, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Molecular characterization of a series of 990 index patients with albinism.

Lasseaux E, Plaisant C, Michaud V, Pennamen P, Trimouille A, Gaston L, Monfermé S, Lacombe D, Rooryck C, Morice-Picard F, Arveiler B.

Pigment Cell Melanoma Res. 2018 Jul;31(4):466-474. doi: 10.1111/pcmr.12688. Epub 2018 Feb 14.

PubMed [citation]
PMID:
29345414

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004240913.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: OCA2 c.1465A>G (p.Asn489Asp) results in a conservative amino acid change located in the Citrate transporter-like domain (IPR004680) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00035 in 251496 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in OCA2 causing Oculocutaneous Albinism (0.00035 vs 0.0043), allowing no conclusion about variant significance. c.1465A>G has been reported in the literature in multiple individuals affected with Oculocutaneous Albinism (example: Lasseaux_2018). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 29345414). Eleven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024