NM_031885.5(BBS2):c.239C>T (p.Ala80Val) AND Bardet-Biedl syndrome

Clinical significance:Uncertain significance (Last evaluated: Jul 1, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001348618.1

Allele description [Variation Report for NM_031885.5(BBS2):c.239C>T (p.Ala80Val)]

NM_031885.5(BBS2):c.239C>T (p.Ala80Val)

Gene:
BBS2:Bardet-Biedl syndrome 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q13
Genomic location:
Preferred name:
NM_031885.5(BBS2):c.239C>T (p.Ala80Val)
HGVS:
  • NC_000016.10:g.56514559G>A
  • NG_009312.1:g.10725C>T
  • NG_009312.2:g.10466C>T
  • NM_001377456.1:c.239C>T
  • NM_031885.5:c.239C>TMANE SELECT
  • NP_001364385.1:p.Ala80Val
  • NP_114091.4:p.Ala80Val
  • NC_000016.9:g.56548471G>A
  • NR_165293.1:n.401C>T
  • NR_165294.1:n.401C>T
  • NR_165295.1:n.401C>T
  • NR_165296.1:n.401C>T
  • NR_165297.1:n.401C>T
Protein change:
A80V
Molecular consequence:
  • NM_001377456.1:c.239C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_031885.5:c.239C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_165293.1:n.401C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165294.1:n.401C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165295.1:n.401C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165296.1:n.401C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165297.1:n.401C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Bardet-Biedl syndrome (BBS)
Identifiers:
MONDO: MONDO:0015229; MedGen: C0752166; Orphanet: 110; OMIM: PS209900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001542925Invitaecriteria provided, single submitter
Uncertain significance
(Jul 1, 2020)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001542925.1

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

Description

This sequence change replaces alanine with valine at codon 80 of the BBS2 protein (p.Ala80Val). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and valine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with BBS2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Benign; Align-GVGD: Class C0). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.

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

Last Updated: Oct 7, 2021

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