NM_012452.3(TNFRSF13B):c.298dup (p.Cys100fs) AND Immunodeficiency, common variable, 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 4, 2023
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:: RCV001946976.6

Allele description [Variation Report for NM_012452.3(TNFRSF13B):c.298dup (p.Cys100fs)]

NM_012452.3(TNFRSF13B):c.298dup (p.Cys100fs)

Gene:

TNFRSF13B:TNF receptor superfamily member 13B [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_012452.3(TNFRSF13B):c.298dup (p.Cys100fs)

HGVS:

NC_000017.11:g.16948885dup
NG_007281.1:g.28204dup
NM_012452.2:c.298dupT
NM_012452.3:c.298dupMANE SELECT
NP_036584.1:p.Cys100fs
LRG_120t1:c.298dup
LRG_120:g.28204dup
NC_000017.10:g.16852198_16852199insA
NC_000017.10:g.16852199dup

Protein change:

C100fs

Links:

dbSNP: rs72553878

NCBI 1000 Genomes Browser:

rs72553878

Molecular consequence:

NM_012452.3:c.298dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Immunodeficiency, common variable, 2
Synonyms:: ANTIBODY DEFICIENCY DUE TO TACI DEFECT; HYPOGAMMAGLOBULINEMIA DUE TO TACI DEFICIENCY; Hypogamma-globulinemia, acquired; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009413; MedGen: C3150354; Orphanet: 1572; OMIM: 240500

Recent activity

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Mus musculus SRY-box containing gene 8 (Sox8), mRNA
Mus musculus SRY-box containing gene 8 (Sox8), mRNA
gi|33563275|ref|NM_011447.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002242759	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 4, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16007087, 27123465, 18981294, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002242759

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 4, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans.

Salzer U, Chapel HM, Webster AD, Pan-Hammarström Q, Schmitt-Graeff A, Schlesier M, Peter HH, Rockstroh JK, Schneider P, Schäffer AA, Hammarström L, Grimbacher B.

Nat Genet. 2005 Aug;37(8):820-8. Epub 2005 Jul 10.

PubMed [citation]

PMID:: 16007087

Clinical Associations of Biallelic and Monoallelic TNFRSF13B Variants in Italian Primary Antibody Deficiency Syndromes.

Pulvirenti F, Zuntini R, Milito C, Specchia F, Spadaro G, Danieli MG, Pession A, Quinti I, Ferrari S.

J Immunol Res. 2016;2016:8390356. doi: 10.1155/2016/8390356. Epub 2016 Mar 30.

PubMed [citation]

PMID:: 27123465
PMCID:: PMC4829724

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002242759.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Cys100Leufs*6) in the TNFRSF13B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TNFRSF13B are known to be pathogenic (PMID: 16007087, 27123465). This variant is present in population databases (rs774205573, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with common variable immunodeficiency (PMID: 18981294). ClinVar contains an entry for this variant (Variation ID: 1456816). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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