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NM_000329.3(RPE65):c.131G>A (p.Arg44Gln) AND Retinitis pigmentosa 20

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 3, 2022
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:
RCV001808321.1

Allele description [Variation Report for NM_000329.3(RPE65):c.131G>A (p.Arg44Gln)]

NM_000329.3(RPE65):c.131G>A (p.Arg44Gln)

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.131G>A (p.Arg44Gln)
HGVS:
  • NC_000001.11:g.68446824C>T
  • NG_008472.2:g.8136G>A
  • NM_000329.3:c.131G>AMANE SELECT
  • NP_000320.1:p.Arg44Gln
  • NC_000001.10:g.68912507C>T
  • NG_008472.1:g.8136G>A
  • NM_000329.2:c.131G>A
  • Q16518:p.Arg44Gln
  • p.(Arg44Gln)
Protein change:
R44Q
Links:
UniProtKB: Q16518#VAR_017128; dbSNP: rs61751282
NCBI 1000 Genomes Browser:
rs61751282
Molecular consequence:
  • NM_000329.3:c.131G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Retinitis pigmentosa 20 (RP20)
Synonyms:
RP 20
Identifiers:
MONDO: MONDO:0013425; MedGen: C3151086; Orphanet: 791; OMIM: 613794

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV0020584353billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 3, 2022)
germlineclinical testing

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

PMID:16150724

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not 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 3billion, SCV002058435.1

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

Description

Same nucleotide change resulting in same amino acid change has been previously reported to be associated with RPE65 related disorder (ClinVar ID: VCV000098840, PMID:11462243, PS1_P). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PMID: 11462243, 15024725, 20079931, PM3_M). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 16150724, 19431183, PS3_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.971, 3CNET: 0.813, PP3_P). A missense variant is a common mechanism associated with Retinitis pigmentosa 20 (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000040, PM2_M).. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Jul 7, 2024