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NM_000283.4(PDE6B):c.1576G>A (p.Glu526Lys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 8, 2021
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:
RCV001857472.5

Allele description [Variation Report for NM_000283.4(PDE6B):c.1576G>A (p.Glu526Lys)]

NM_000283.4(PDE6B):c.1576G>A (p.Glu526Lys)

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.1576G>A (p.Glu526Lys)
HGVS:
  • NC_000004.12:g.660575G>A
  • NG_009839.1:g.40002G>A
  • NM_000283.4:c.1576G>AMANE SELECT
  • NM_001145291.2:c.1576G>A
  • NM_001145292.2:c.739G>A
  • NM_001350154.3:c.739G>A
  • NM_001350155.3:c.421G>A
  • NM_001379246.1:c.739G>A
  • NM_001379247.1:c.739G>A
  • NP_000274.2:p.Glu526Lys
  • NP_000274.3:p.Glu526Lys
  • NP_001138763.2:p.Glu526Lys
  • NP_001138764.2:p.Glu247Lys
  • NP_001337083.1:p.Glu247Lys
  • NP_001337084.1:p.Glu141Lys
  • NP_001366175.1:p.Glu247Lys
  • NP_001366176.1:p.Glu247Lys
  • NC_000004.11:g.654364G>A
  • NM_000283.3:c.1576G>A
Protein change:
E141K
Links:
dbSNP: rs527236091
NCBI 1000 Genomes Browser:
rs527236091
Molecular consequence:
  • NM_000283.4:c.1576G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145291.2:c.1576G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145292.2:c.739G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350154.3:c.739G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350155.3:c.421G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379246.1:c.739G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379247.1:c.739G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002171448Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jun 8, 2021)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Comprehensive molecular diagnosis of a large cohort of Japanese retinitis pigmentosa and Usher syndrome patients by next-generation sequencing.

Oishi M, Oishi A, Gotoh N, Ogino K, Higasa K, Iida K, Makiyama Y, Morooka S, Matsuda F, Yoshimura N.

Invest Ophthalmol Vis Sci. 2014 Oct 16;55(11):7369-75. doi: 10.1167/iovs.14-15458.

PubMed [citation]
PMID:
25324289

Molecular genetic analysis using targeted NGS analysis of 677 individuals with retinal dystrophy.

Jespersgaard C, Fang M, Bertelsen M, Dang X, Jensen H, Chen Y, Bech N, Dai L, Rosenberg T, Zhang J, Møller LB, Tümer Z, Brøndum-Nielsen K, Grønskov K.

Sci Rep. 2019 Feb 4;9(1):1219. doi: 10.1038/s41598-018-38007-2.

PubMed [citation]
PMID:
30718709
PMCID:
PMC6362094
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002171448.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individual(s) with autosomal recessive retinitis pigmentosa (PMID: 25324289, 30718709). ClinVar contains an entry for this variant (Variation ID: 143066). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with lysine at codon 526 of the PDE6B protein (p.Glu526Lys). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and lysine.

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

Last Updated: Sep 29, 2024