NM_000275.3(OCA2):c.1080C>T (p.Ser360=) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 9, 2024
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:: RCV001854952.3

Allele description [Variation Report for NM_000275.3(OCA2):c.1080C>T (p.Ser360=)]

NM_000275.3(OCA2):c.1080C>T (p.Ser360=)

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.1080C>T (p.Ser360=)

HGVS:

NC_000015.10:g.27990612G>A
NG_009846.1:g.113701C>T
NM_000275.3:c.1080C>TMANE SELECT
NM_001300984.2:c.1045-946C>T
NP_000266.2:p.Ser360=
NC_000015.9:g.28235758G>A
NM_000275.2:c.1080C>T

Links:

dbSNP: rs373775562

NCBI 1000 Genomes Browser:

rs373775562

Molecular consequence:

NM_001300984.2:c.1045-946C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000275.3:c.1080C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002125453	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 9, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 37650133, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002125453

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 9, 2024)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Unsuspected consequences of synonymous and missense variants in OCA2 can be detected in blood cell RNA samples of patients with albinism.

Michaud V, Sequeira A, Mercier E, Lasseaux E, Plaisant C, Hadj-Rabia S, Whalen S, Bonneau D, Dieux-Coeslier A, Morice-Picard F, Coursimault J, Arveiler B, Javerzat S.

Pigment Cell Melanoma Res. 2023 Aug 31. doi: 10.1111/pcmr.13123. [Epub ahead of print]

PubMed [citation]

PMID:: 37650133

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002125453.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change affects codon 360 of the OCA2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the OCA2 protein. This variant is present in population databases (rs373775562, gnomAD 0.004%). This variant has been observed in individual(s) with clinical features of oculocutaneous albinism (PMID: 37650133; Invitae). 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: 255717). Studies have shown that this variant is associated with inconclusive levels of altered splicing (PMID: 37650133). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 10, 2024

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