NM_019098.5(CNGB3):c.467C>T (p.Ser156Phe) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Dec 3, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000815424.1

Allele description [Variation Report for NM_019098.5(CNGB3):c.467C>T (p.Ser156Phe)]

NM_019098.5(CNGB3):c.467C>T (p.Ser156Phe)

Gene:
CNGB3:cyclic nucleotide gated channel subunit beta 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q21.3
Genomic location:
Preferred name:
NM_019098.5(CNGB3):c.467C>T (p.Ser156Phe)
HGVS:
  • NC_000008.11:g.86670970G>A
  • NG_016980.1:g.77706C>T
  • NM_019098.4:c.467C>T
  • NM_019098.5:c.467C>TMANE SELECT
  • NP_061971.3:p.Ser156Phe
  • NP_061971.3:p.Ser156Phe
  • NC_000008.10:g.87683198G>A
Protein change:
S156F
Links:
dbSNP: rs139207764
NCBI 1000 Genomes Browser:
rs139207764
Molecular consequence:
  • NM_019098.4:c.467C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_019098.5:c.467C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000955875Invitaecriteria provided, single submitter
Likely pathogenic
(Dec 3, 2018)
germlineclinical testing

PubMed (5)
[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

CNGB3 mutation spectrum including copy number variations in 552 achromatopsia patients.

Mayer AK, Van Cauwenbergh C, Rother C, Baumann B, Reuter P, De Baere E, Wissinger B, Kohl S; ACHM Study Group..

Hum Mutat. 2017 Nov;38(11):1579-1591. doi: 10.1002/humu.23311. Epub 2017 Aug 28.

PubMed [citation]
PMID:
28795510

CNGB3 mutations account for 50% of all cases with autosomal recessive achromatopsia.

Kohl S, Varsanyi B, Antunes GA, Baumann B, Hoyng CB, Jägle H, Rosenberg T, Kellner U, Lorenz B, Salati R, Jurklies B, Farkas A, Andreasson S, Weleber RG, Jacobson SG, Rudolph G, Castellan C, Dollfus H, Legius E, Anastasi M, Bitoun P, Lev D, et al.

Eur J Hum Genet. 2005 Mar;13(3):302-8.

PubMed [citation]
PMID:
15657609
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000955875.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change replaces serine with phenylalanine at codon 156 of the CNGB3 protein (p.Ser156Phe). The serine residue is highly conserved and there is a large physicochemical difference between serine and phenylalanine. This variant is present in population databases (rs139207764, ExAC 0.01%). This variant has been observed in individuals with achromatopsia (PMID: 25616768, 15657609, 28795510). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 427671). This variant has been reported to have insufficient data to determine the effect on CNGB3 protein function (PMID: 26106334). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Nov 20, 2021

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