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NM_000275.3(OCA2):c.1327G>A (p.Val443Ile) AND Tyrosinase-positive oculocutaneous albinism

Germline classification:
Pathogenic/Likely pathogenic (17 submissions)
Last evaluated:
Dec 21, 2023
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:
RCV000001006.47

Allele description [Variation Report for NM_000275.3(OCA2):c.1327G>A (p.Val443Ile)]

NM_000275.3(OCA2):c.1327G>A (p.Val443Ile)

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.1327G>A (p.Val443Ile)
HGVS:
  • NC_000015.10:g.27985101C>T
  • NG_009846.1:g.119212G>A
  • NM_000275.3:c.1327G>AMANE SELECT
  • NM_001300984.2:c.1255G>A
  • NP_000266.2:p.Val443Ile
  • NP_001287913.1:p.Val419Ile
  • NC_000015.9:g.28230247C>T
  • NM_000275.2:c.1327G>A
  • Q04671:p.Val443Ile
Protein change:
V419I; VAL443ILE
Links:
UniProtKB: Q04671#VAR_006132; OMIM: 611409.0004; dbSNP: rs121918166
NCBI 1000 Genomes Browser:
rs121918166
Molecular consequence:
  • NM_000275.3:c.1327G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001300984.2:c.1255G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000021156OMIM
no assertion criteria provided
Pathogenic
(Feb 24, 1994)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000248365Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 17, 2015)
germlineclinical testing

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

SCV000390147Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Pathogenic
(Apr 5, 2019)
germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

Citation Link,

SCV000584106HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha
criteria provided, single submitter

(HA_assertions_20150911)
Pathogenic
(Sep 11, 2014)
paternalresearch

HA_assertions_20150911.pdf,

Citation Link,

SCV000966900Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Pathogenic
(Feb 6, 2018)
germlineclinical testing

PubMed (15)
[See all records that cite these PMIDs]

SCV001139535Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Pathogenic
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001142446Reproductive Health Research and Development, BGI Genomics
no assertion criteria provided
Pathogenic
(Jan 6, 2020)
germlinecuration

SCV001760341Genomics England Pilot Project, Genomics England
no assertion criteria provided

(ACGS Guidelines, 2016)
Likely pathogenicgermlineclinical testing

Citation Link,

SCV002039331Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 7, 2021)
germlineclinical testing

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

SCV002572351Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Aug 26, 2022)
germlineclinical testing

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

Citation Link,

SCV002581646MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 18, 2022)
germlineclinical testing

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

SCV002768880Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 21, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV003804566Laboratoire de Génétique Moléculaire, CHU Bordeaux
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

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

SCV004099434Zotz-Klimas Genetics Lab, MVZ Zotz Klimas
no assertion criteria provided
Pathogenic
(Oct 30, 2023)
germlineclinical testing

SCV004177044Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 22, 2023)
germlineclinical testing

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

SCV004244523Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 4, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes5not providednot providednot providednot providedclinical testing
not providedpaternalyes2not providednot provided2not providedresearch
not providedgermlinenot provided11not providednot providednot providedliterature only, clinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Absence of predictable phenotypic expression in proximal 15q duplications.

Ludowese CJ, Thompson KJ, Sekhon GS, Pauli RM.

Clin Genet. 1991 Sep;40(3):194-201.

PubMed [citation]
PMID:
1773534

MIR204 n.37C>T variant as a cause of chorioretinal dystrophy variably associated with iris coloboma, early-onset cataracts and congenital glaucoma.

Jedlickova J, Vajter M, Barta T, Black GCM, Perveen R, Mares J, Fichtl M, Kousal B, Dudakova L, Liskova P.

Clin Genet. 2023 Oct;104(4):418-426. doi: 10.1111/cge.14391. Epub 2023 Jun 15.

PubMed [citation]
PMID:
37321975
See all PubMed Citations (22)

Details of each submission

From OMIM, SCV000021156.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a 4-year-old boy of northern European ancestry with typical type II oculocutaneous albinism (OCA2; 203200), Lee et al. (1994) identified compound heterozygosity for 2 mutations in the OCA2 gene: a G-to-A transition, resulting in a val443-to-ile (V443I) substitution inherited from the mother, and a C-to-T transition in exon 22 resulting in a pro743-to-leu (P743L; 611409.0005) substitution inherited from the father. The patient's skin was very lightly pigmented with no apparent tanning ability, and his hair was pale golden yellow. His irides were blue and showed transillumination, and the fundi appeared nonpigmented, with hypoplastic maculae. His corrected visual acuity was 20/100, and he had nystagmus and strabismus. Chromosomal analysis demonstrated mosaicism for 46,XY and 46,XY,dup(15)(q12). The duplication, which occurred in 25% of stimulated peripheral-blood leukocytes, was interpreted as a nonpathologic chromosomal variant (Ludowese et al., 1991). Lee et al. (1994) found the same V443I substitution on the maternally derived chromosome 15 in a 7-year-old boy with typical type II oculocutaneous albinism and Prader-Willi syndrome (PWS; 176270), the latter being due to deletion of 15q11.2-q13.1 derived from the father. The paternal OCA2 gene was deleted in this child.

In a mother and 3 of her children in a Czech family with oculocutaneous or ocular albinism, Jedlickova et al. (2023) identified homozygosity or compound heterozygosity for the V443I mutation in the OCA2 gene. The mother and a daughter, who both had oculocutaneous albinism, were compound heterozygous for V443I and a large complex rearrangement in the OCA2 gene, whereas the 2 sons, who had ocular albinism, were homozygous for the V443I substitution. The authors noted that the sons had normal visual acuity with discrete fundus hypopigmentation and foveal hypoplasia, which was only revealed due to the familial investigation; they suggested that these findings supported the notion of V443I as a hypomorphic allele causing only a partial loss of function, thus accounting for the 4 homozygous individuals present in the gnomAD database (v2.1.1).

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

From Genetic Services Laboratory, University of Chicago, SCV000248365.1

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

From Illumina Laboratory Services, Illumina, SCV000390147.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

The OCA2 c.1327G>A (p.Val443Ile) missense variant has been described as the most common pathogenic variant for oculocutaneous albinism type 2 (OCA) in northern European populations (Lewis et al. 2012). Across a selection of the literature, the p.Val443Ile variant has been reported in at least six studies in which it is found in a total of 15 patients with OCA, including in two in a homozygous state, in ten in a compound heterozygous state, and in three in a heterozygous state (Lee et al. 1994; Oetting et al. 2005; Hutton et al. 2008; Gargiulo et al. 2011; Zhang et al. 2013; Wei et al. 2015). One homozygote and one compound heterozygote also carried variants in other OCA-related genes. In at least three families, unaffected parents were found to be heterozygous for the p.Val443Ile variant. Control data are unavailable for this variant, which is reported at a frequency of 0.00628 in the European American population of the Exome Sequencing Project. Functional studies demonstrated that the p.Val443Ile variant protein localized similarly to wild type but showed reduced activity of 85% and reduced pH regulation compared to wild-type (Bellono et al. 2014). Based on the collective evidence, the p.Val443Ile variant is classified as pathogenic for oculocutaneous albinism. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha, SCV000584106.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearchnot provided
2not provided1not providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyes1not providednot provided1not providednot providednot provided
2paternalyes1not providednot provided1not providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000966900.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (15)

Description

The p.Val443Ile variant in OCA2 has been reported in the homozygous or compound heterozygous state in >10 individuals with oculocutaneous albinism (OCA) type 2, including 1 de novo occurrence (Oetting 2005, Hutton 2008, Gargiulo 2011, Zhang 2013, Wolfson 2016, Andersen 2016, Gao 2017). This variant is reported to be th e most common pathogenic OCA2 variant in northern European populations (Hutton 2 008, Lewis 2012) and has been identified in 0.5% (639/125694) of European chromo somes, including 4 homozygous individuals, by the Genome Aggregation Database (g nomAD, http://gnomad.broadinstitute.org; dbSNP rs121918166). This frequency is c onsistent with the carrier frequency for OCA type 2. In vitro studies demonstrat ed that the p.Val443Ile variant results in a partial loss of protein function (S viderskaya 1997, Bellono 2014). In summary, this variant meets criteria to be cl assified as pathogenic for OCA type 2 in an autosomal recessive manner. ACMG/AMP Criteria applied: PM3_Very Strong; PM6; PS3_Supporting; PP4.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

From Mendelics, SCV001139535.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Reproductive Health Research and Development, BGI Genomics, SCV001142446.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_000275.2:c.1327G>A in the OCA2 gene has an allele frequency of 0.005 in European (no Finnish) subpopulation in the gnomAD database. Functional studies demonstrate that the V443I variant disrupts ion conductance, which is required for melanin production (PMID: 27231233). It was detected in multiple individuals with autosomal recessive Oculocutaneous albinism, two homozygous for this variant, compound heterozygous with c.2228C>T, c.1465A>G, Deletion 15q11.2-q13.1, repectively (PMID: 18463683). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP criteria applied: PM3_VeryStrong; PS3; PP4.

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

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001370164.2

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

Description

This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PM3,PP3,PP4,PP5,BS2.

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

From Genomics England Pilot Project, Genomics England, SCV001760341.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome-Nilou Lab, SCV002039331.1

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002572351.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: OCA2 c.1327G>A (p.Val443Ile) 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 0.003 in 250050 control chromosomes in the gnomAD database, including 3 homozygotes. This frequency does not allow conclusions about variant significance. c.1327G>A has been widely reported in the literature as a homozygous or compound heterozygous genotype in multiple individuals affected with Oculocutaneous Albinism (example, Lasseaux_2018). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (example, Bellono_2014). The most pronounced variant effect results in near abolishment of normal ion channel activity as measured by OCA2-mediated chloride current measurements in-vitro. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 with a predominant consensus as pathogenic (n=15, VUS, n=1). 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

From MGZ Medical Genetics Center, SCV002581646.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided5not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002768880.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as pathogenic. The following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with brown oculocutaneous albinism (MIM#203200) and oculocutaneous albinism, type II (MIM#203200). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 24518832; OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from valine to isoleucine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2) (852 heterozygotes, 4 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated citrate transporter domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. p.(Val443Ile) is a well-reported variant associated with oculocutaneous albinism and has previously been reported in more than ten individuals with a clinical diagnosis of oculocutaneous albinism, in homozygous and compound heterozygous state (PMID: 31196117, PMID: 18463683) (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

From Laboratoire de Génétique Moléculaire, CHU Bordeaux, SCV003804566.1

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

From Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004099434.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV004177044.1

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

Description

The OCA2 c.1327G>A (p.Val443Ile) variant has been reported in the homozygous and compound heterozygous state in many individuals affected with oculocutaneous albinism and is reported to be the most common pathogenic OCA2 variant in individuals of European ancestry (Andersen JD et al., PMID: 27468418; Gao J et al., PMID: 28451379; Gargiulo A et al., PMID: 20861488; Hutton SM et al., PMID: 18463683; Oetting WS et al., PMID: 15712365; Wolfson Y et al., PMID: 26474496). This variant has been reported in the ClinVar database as a germline pathogenic variant by more than 20 submitters. The highest population minor allele frequency in the genome aggregation database (v.2.1.1) is 0.5% in the European population which is consistent with the carrier frequency of oculocutaneous albinism (Grønskov K et al., PMID: 17980020). Computational predictors indicate that the variant is damaging, evidence that correlates with impact to OCA2 function. In support of this prediction, functional studies show the variant reduced protein function and altered protein localization (Bellono NW et al., PMID: 25513726; Sviderskaya EV et al., PMID: 8980282). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as pathogenic.

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

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV004244523.1

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

Description

PS3, PP3, PM3_Strong, PM6

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

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001370164Centre for Mendelian Genomics, University Medical Centre Ljubljana
flagged submission
Reason: Older claim that does not account for recent evidence
Notes: None

(ACMG Guidelines, 2015)
Uncertain significance
(Jan 1, 2016)
unknownclinical testing

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

Last Updated: Nov 10, 2024