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NM_000440.3(PDE6A):c.1705C>A (p.Gln569Lys) AND PDE6A-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 9, 2023
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:
RCV003416002.4

Allele description [Variation Report for NM_000440.3(PDE6A):c.1705C>A (p.Gln569Lys)]

NM_000440.3(PDE6A):c.1705C>A (p.Gln569Lys)

Gene:
PDE6A:phosphodiesterase 6A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_000440.3(PDE6A):c.1705C>A (p.Gln569Lys)
HGVS:
  • NC_000005.10:g.149895206G>T
  • NG_009102.1:g.54588C>A
  • NM_000440.3:c.1705C>AMANE SELECT
  • NP_000431.2:p.Gln569Lys
  • NC_000005.9:g.149274769G>T
  • NM_000440.2:c.1705C>A
  • P16499:p.Gln569Lys
Protein change:
Q569K
Links:
UniProtKB: P16499#VAR_025466; dbSNP: rs139444207
NCBI 1000 Genomes Browser:
rs139444207
Molecular consequence:
  • NM_000440.3:c.1705C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
PDE6A-related disorder
Synonyms:
PDE6A-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004115983PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 9, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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, SCV004115983.1

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

Description

The PDE6A c.1705C>A variant is predicted to result in the amino acid substitution p.Gln569Lys. This variant has been reported many times in the compound heterozygous state in individuals with retinitis pigmentosa (see for examples Bryant et al. 2017. PubMed ID: 29343940; Ezquerra-Inchausti et al. 2018. PubMed ID: 30337596; Table S2 in Zampaglione et al. 2020. PubMed ID: 32037395). This variant is reported in 0.028% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/5-149274769-G-T). Given the evidence, we interpret c.1705C>A (p.Gln569Lys) as pathogenic.

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

Last Updated: Sep 16, 2024