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NM_000283.4(PDE6B):c.1624C>T (p.Arg542Trp) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 5, 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:
RCV001053317.8

Allele description [Variation Report for NM_000283.4(PDE6B):c.1624C>T (p.Arg542Trp)]

NM_000283.4(PDE6B):c.1624C>T (p.Arg542Trp)

Gene:
PDE6B:phosphodiesterase 6B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
NM_000283.4(PDE6B):c.1624C>T (p.Arg542Trp)
HGVS:
  • NC_000004.12:g.662143C>T
  • NG_009839.1:g.41570C>T
  • NM_000283.4:c.1624C>TMANE SELECT
  • NM_001145291.2:c.1624C>T
  • NM_001145292.2:c.787C>T
  • NM_001350154.3:c.787C>T
  • NM_001350155.3:c.469C>T
  • NM_001379246.1:c.787C>T
  • NM_001379247.1:c.787C>T
  • NP_000274.2:p.Arg542Trp
  • NP_000274.3:p.Arg542Trp
  • NP_001138763.2:p.Arg542Trp
  • NP_001138764.2:p.Arg263Trp
  • NP_001337083.1:p.Arg263Trp
  • NP_001337084.1:p.Arg157Trp
  • NP_001366175.1:p.Arg263Trp
  • NP_001366176.1:p.Arg263Trp
  • NC_000004.11:g.655932C>T
  • NM_000283.3:c.1624C>T
Protein change:
R157W
Links:
dbSNP: rs760042062
NCBI 1000 Genomes Browser:
rs760042062
Molecular consequence:
  • NM_000283.4:c.1624C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145291.2:c.1624C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145292.2:c.787C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350154.3:c.787C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350155.3:c.469C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379246.1:c.787C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379247.1:c.787C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001217575Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 5, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Dependable and efficient clinical utility of target capture-based deep sequencing in molecular diagnosis of retinitis pigmentosa.

Wang J, Zhang VW, Feng Y, Tian X, Li FY, Truong C, Wang G, Chiang PW, Lewis RA, Wong LJ.

Invest Ophthalmol Vis Sci. 2014 Aug 5;55(10):6213-23. doi: 10.1167/iovs.14-14936.

PubMed [citation]
PMID:
25097241

Cone Spacing Correlates With Retinal Thickness and Microperimetry in Patients With Inherited Retinal Degenerations.

Foote KG, De la Huerta I, Gustafson K, Baldwin A, Zayit-Soudry S, Rinella N, Porco TC, Roorda A, Duncan JL.

Invest Ophthalmol Vis Sci. 2019 Mar 1;60(4):1234-1243. doi: 10.1167/iovs.18-25688.

PubMed [citation]
PMID:
30924848
PMCID:
PMC6440525
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001217575.5

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 542 of the PDE6B protein (p.Arg542Trp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of autosomal recessive retinal dystrophy (PMID: 25097241, 30924848, 33691693; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 849373). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PDE6B protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024