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NM_031885.5(BBS2):c.2107C>T (p.Arg703Ter) AND Retinitis pigmentosa 74

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
May 22, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001376258.2

Allele description [Variation Report for NM_031885.5(BBS2):c.2107C>T (p.Arg703Ter)]

NM_031885.5(BBS2):c.2107C>T (p.Arg703Ter)

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.2107C>T (p.Arg703Ter)
HGVS:
  • NC_000016.10:g.56484820G>A
  • NG_009312.2:g.40205C>T
  • NM_001377456.1:c.2107C>T
  • NM_031885.5:c.2107C>TMANE SELECT
  • NP_001364385.1:p.Arg703Ter
  • NP_114091.3:p.Arg703Ter
  • NP_114091.4:p.Arg703Ter
  • NC_000016.9:g.56518732G>A
  • NG_009312.1:g.40464C>T
  • NM_031885.3:c.2107C>T
  • NM_031885.4:c.2107C>T
  • NR_165293.1:n.2397C>T
  • NR_165294.1:n.2394C>T
  • NR_165295.1:n.2225C>T
  • NR_165296.1:n.2097C>T
  • NR_165297.1:n.2097C>T
Protein change:
R703*
Links:
dbSNP: rs567573386
NCBI 1000 Genomes Browser:
rs567573386
Molecular consequence:
  • NR_165293.1:n.2397C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165294.1:n.2394C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165295.1:n.2225C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165296.1:n.2097C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165297.1:n.2097C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001377456.1:c.2107C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_031885.5:c.2107C>T - nonsense - [Sequence Ontology: SO:0001587]
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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001573337Ocular Genomics Institute, Massachusetts Eye and Ear
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Apr 8, 2021) 		germlineresearch

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

SCV0025211023billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(May 22, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedresearch, clinical testing

Citations

PubMed

BBS genotype-phenotype assessment of a multiethnic patient cohort calls for a revision of the disease definition.

Deveault C, Billingsley G, Duncan JL, Bin J, Theal R, Vincent A, Fieggen KJ, Gerth C, Noordeh N, Traboulsi EI, Fishman GA, Chitayat D, Knueppel T, Millán JM, Munier FL, Kennedy D, Jacobson SG, Innes AM, Mitchell GA, Boycott K, Héon E.

Hum Mutat. 2011 Jun;32(6):610-9. doi: 10.1002/humu.21480. Epub 2011 Mar 22.

PubMed [citation]
PMID:
21344540

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 Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001573337.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)

Description

The BBS2 c.2107C>T variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2. Based on this evidence we have classified this variant as Likely Pathogenic.

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

From 3billion, SCV002521102.1

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

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.003%). Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through protein truncation. The predicted truncated protein may be shortened by less than 10%. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000496478 / PMID: 21344540). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Nov 24, 2024