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NM_031885.5(BBS2):c.118G>T (p.Val40Phe) AND Retinitis pigmentosa 74

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 22, 2022
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:
RCV002250616.1

Allele description [Variation Report for NM_031885.5(BBS2):c.118G>T (p.Val40Phe)]

NM_031885.5(BBS2):c.118G>T (p.Val40Phe)

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.118G>T (p.Val40Phe)
HGVS:
  • NC_000016.10:g.56514680C>A
  • NG_009312.2:g.10345G>T
  • NM_001377456.1:c.118G>T
  • NM_031885.5:c.118G>TMANE SELECT
  • NP_001364385.1:p.Val40Phe
  • NP_114091.4:p.Val40Phe
  • NC_000016.9:g.56548592C>A
  • NG_009312.1:g.10604G>T
  • NM_031885.3:c.118G>T
  • NR_165293.1:n.280G>T
  • NR_165294.1:n.280G>T
  • NR_165295.1:n.280G>T
  • NR_165296.1:n.280G>T
  • NR_165297.1:n.280G>T
Protein change:
V40F
Links:
dbSNP: rs886043059
NCBI 1000 Genomes Browser:
rs886043059
Molecular consequence:
  • NM_001377456.1:c.118G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_031885.5:c.118G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_165293.1:n.280G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165294.1:n.280G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165295.1:n.280G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165296.1:n.280G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165297.1:n.280G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Retinitis pigmentosa 74 (RP74)
Identifiers:
MONDO: MONDO:0014692; MedGen: C4225281; Orphanet: 791; OMIM: 616562

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV0025210593billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(May 22, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease.

Stone EM, Andorf JL, Whitmore SS, DeLuca AP, Giacalone JC, Streb LM, Braun TA, Mullins RF, Scheetz TE, Sheffield VC, Tucker BA.

Ophthalmology. 2017 Sep;124(9):1314-1331. doi: 10.1016/j.ophtha.2017.04.008. Epub 2017 May 27.

PubMed [citation]
PMID:
28559085
PMCID:
PMC5565704

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 3billion, SCV002521059.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. Protein truncation variants are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.88; 3Cnet: 3CNET). Same nucleotide change resulting in same amino acid change has been previously reported to be associated with BBS2 related disorder (ClinVar ID: VCV000285263 / PMID: 28559085). However, the evidence of pathogenicity is insufficient at this time. Therefore, this variant is classified as uncertain significanceaccording to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Jun 23, 2024