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NM_052945.4(TNFRSF13C):c.142G>A (p.Ala48Thr) AND Immunodeficiency, common variable, 4

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 8, 2021
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:
RCV001950658.4

Allele description [Variation Report for NM_052945.4(TNFRSF13C):c.142G>A (p.Ala48Thr)]

NM_052945.4(TNFRSF13C):c.142G>A (p.Ala48Thr)

Genes:
LOC130067574:ATAC-STARR-seq lymphoblastoid silent region 13813 [Gene]
TNFRSF13C:TNF receptor superfamily member 13C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.2
Genomic location:
Preferred name:
NM_052945.4(TNFRSF13C):c.142G>A (p.Ala48Thr)
HGVS:
  • NC_000022.11:g.41926326C>T
  • NG_007579.1:g.5492G>A
  • NM_052945.4:c.142G>AMANE SELECT
  • NP_443177.1:p.Ala48Thr
  • LRG_184:g.5492G>A
  • NC_000022.10:g.42322330C>T
Protein change:
A48T
Links:
dbSNP: rs1407623179
NCBI 1000 Genomes Browser:
rs1407623179
Molecular consequence:
  • NM_052945.4:c.142G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Immunodeficiency, common variable, 4
Synonyms:
ANTIBODY DEFICIENCY DUE TO BAFFR DEFECT
Identifiers:
MONDO: MONDO:0013284; MedGen: C3150739; Orphanet: 1572; OMIM: 613494

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002225163Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 8, 2021) 		germlineclinical testing

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

Help

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002225163.3

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

Description

This sequence change replaces alanine with threonine at codon 48 of the TNFRSF13C protein (p.Ala48Thr). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and threonine. 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with TNFRSF13C-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database.

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

Last Updated: Sep 29, 2024