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NM_000275.3(OCA2):c.1080C>T (p.Ser360=) AND Tyrosinase-positive oculocutaneous albinism

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Sep 4, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV003128241.3

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)

Name:
Tyrosinase-positive oculocutaneous albinism (OCA2)
Synonyms:
ALBINISM II; Albinism 2; Albinoidism; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008746; MedGen: C0268495; Orphanet: 79432; OMIM: 203200

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000303416PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Sep 4, 2024) 		germlineclinical testing

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

SCV003804576Laboratoire de Génétique Moléculaire, CHU Bordeaux
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV000303416.2

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

Description

This variant has been reported in eight unrelated individuals, six of them in the compound heterozygous state, in a cohort study of oculocutaneous albinism (Michaud et al. 2023. PubMed ID: 37650133). While this variant is not predicted to affect splicing (SpliceAI, Jaganathan et al. 2019. PubMed ID: 30661751), a functional study using both a minigene splicing assay and RT-PCR analysis of patient blood samples demonstrated that the c.1080C>T variant increases the skipping of exon 10 in the transcript, which is predicted to result in a non-functional protein (Michaud et al. 2023. PubMed ID: 37650133). This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD. This variant is interpreted as likely pathogenic.

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

From Laboratoire de Génétique Moléculaire, CHU Bordeaux, SCV003804576.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024