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NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg) AND TNFRSF13B-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 27, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003398448.7

Allele description [Variation Report for NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)]

NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)

Gene:
TNFRSF13B:TNF receptor superfamily member 13B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p11.2
Genomic location:
Preferred name:
NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)
HGVS:
  • NC_000017.11:g.16948873A>G
  • NG_007281.1:g.28216T>C
  • NM_012452.3:c.310T>CMANE SELECT
  • NP_036584.1:p.Cys104Arg
  • NP_036584.1:p.Cys104Arg
  • LRG_120t1:c.310T>C
  • LRG_120:g.28216T>C
  • LRG_120p1:p.Cys104Arg
  • NC_000017.10:g.16852187A>G
  • NM_012452.2:c.310T>C
  • NM_012452.3:c.310T>C
  • O14836:p.Cys104Arg
  • p.(Cys104Arg)
Protein change:
C104R; CYS104ARG
Links:
UniProtKB: O14836#VAR_024027; OMIM: 604907.0001; dbSNP: rs34557412
NCBI 1000 Genomes Browser:
rs34557412
Molecular consequence:
  • NM_012452.3:c.310T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
TNFRSF13B-related disorder
Synonyms:
TNFRSF13B-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004104594PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Sep 27, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004104594.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The TNFRSF13B c.310T>C variant is predicted to result in the amino acid substitution p.Cys104Arg. This variant has previously been reported to be causative for both autosomal dominant and autosomal recessive forms of common variable immunodeficiency type 2, although autosomal recessive inheritance is more common (Salzer et al. 2005. PubMed ID: 16007087; Romberg et al. 2013. PubMed ID: 24051380). However, the c.310T>C variant has been shown to exhibit incomplete penetrance (Pan-Hammarström et al. 2007. PubMed ID: 17392797; Barroeta Seijas et al. 2012. PubMed ID: 22697072). Functional studies have shown the p.Cys104Arg variant impairs TACI ligand binding and B-cell function (Romberg et al. 2015. PubMed ID: 26100089; Lee et al. 2010. PubMed ID: 20889194). This variant is reported in 0.54% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.

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

Last Updated: Oct 26, 2024