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NM_000329.3(RPE65):c.1302G>A (p.Ala434=) AND RPE65-related recessive retinopathy

Germline classification:
Benign (1 submission)
Last evaluated:
Dec 22, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV003459236.1

Allele description [Variation Report for NM_000329.3(RPE65):c.1302G>A (p.Ala434=)]

NM_000329.3(RPE65):c.1302G>A (p.Ala434=)

Gene:
RPE65:retinoid isomerohydrolase RPE65 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p31.3
Genomic location:
Preferred name:
NM_000329.3(RPE65):c.1302G>A (p.Ala434=)
Other names:
NM_000329.3(RPE65):c.1302G>A; p.Ala434=
HGVS:
  • NC_000001.11:g.68431318C>T
  • NG_008472.2:g.23642G>A
  • NM_000329.3:c.1302G>AMANE SELECT
  • NP_000320.1:p.Ala434=
  • NC_000001.10:g.68897001C>T
  • NG_008472.1:g.23642G>A
  • NM_000329.2:c.1302G>A
Links:
dbSNP: rs62636301
NCBI 1000 Genomes Browser:
rs62636301
Molecular consequence:
  • NM_000329.3:c.1302G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
RPE65-related recessive retinopathy
Synonyms:
Recessive RPE65 retinopathy
Identifiers:
MONDO: MONDO:0100368; MedGen: CN305526

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004190219ClinGen Leber Congenital Amaurosis/early Onset Retinal Dystrophy Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen LCAeoRD ACMG Specifications RPE65 V1.0.0)		Benign
(Dec 22, 2023) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Leber Congenital Amaurosis/early Onset Retinal Dystrophy Variant Curation Expert Panel, ClinGen, SCV004190219.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_000329.3(RPE65):c.1302G>A (p.Ala434=) is a synonymous variant that is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.02695, with 734 alleles / 24954 total alleles and 7 homozygotes in the African/African American population, which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.008 (BA1). The splicing impact predictor SpliceAI gives a delta score of 0.07 for donor loss, which is below the ClinGen LCA / eoRD VCEP recommended threshold of <0.1 and does not predict an impact on splicing (BP4, BP7). In summary, this variant meets the criteria to be classified as Benign for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: BA1, BP4, and BP7. (VCEP specifications version 1.0.0; date of approval 09/21/2023).

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

Last Updated: Sep 29, 2024