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NM_052945.4(TNFRSF13C):c.265_288del (p.Leu89_Val96del) AND Immunodeficiency, common variable, 4

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 18, 2009
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:
RCV000004713.2

Allele description [Variation Report for NM_052945.4(TNFRSF13C):c.265_288del (p.Leu89_Val96del)]

NM_052945.4(TNFRSF13C):c.265_288del (p.Leu89_Val96del)

Genes:
LOC130067574:ATAC-STARR-seq lymphoblastoid silent region 13813 [Gene]
TNFRSF13C:TNF receptor superfamily member 13C [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q13.2
Genomic location:
Preferred name:
NM_052945.4(TNFRSF13C):c.265_288del (p.Leu89_Val96del)
HGVS:
  • NC_000022.11:g.41926180_41926203del
  • NG_007579.1:g.5615_5638del
  • NM_052945.4:c.265_288delMANE SELECT
  • NP_443177.1:p.Leu89_Val96del
  • NP_443177.1:p.Leu89_Val96del
  • LRG_184t1:c.265_288del
  • LRG_184:g.5615_5638del
  • NC_000022.10:g.42322184_42322207del
  • NM_052945.3:c.265_288del
  • NM_052945.3:c.265_288del24
Note:
NCBI staff provided HGVS expressions for allelic variant 606269.0001 based on the assumption that the deletion corresponded to complete codons.
Links:
OMIM: 606269.0001
Molecular consequence:
  • NM_052945.4:c.265_288del - inframe_deletion - [Sequence Ontology: SO:0001822]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000024888OMIM
no assertion criteria provided
Pathogenic
(Aug 18, 2009)
germlineliterature only

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

B-cell activating factor receptor deficiency is associated with an adult-onset antibody deficiency syndrome in humans.

Warnatz K, Salzer U, Rizzi M, Fischer B, Gutenberger S, Böhm J, Kienzler AK, Pan-Hammarström Q, Hammarström L, Rakhmanov M, Schlesier M, Grimbacher B, Peter HH, Eibel H.

Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13945-50. doi: 10.1073/pnas.0903543106. Epub 2009 Aug 6.

PubMed [citation]
PMID:
19666484
PMCID:
PMC2722504

Details of each submission

From OMIM, SCV000024888.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 sibs, born of consanguineous parents, with adult-onset common variable immunodeficiency-4 (613494), Warnatz et al. (2009) identified a homozygous 24-bp in-frame deletion (del89_96) in exon 2 of the TNFRSF13C gene, resulting in the removal of a stretch of 8 hydrophobic amino acids from the transmembrane region. The mutation was not found in 100 controls. The mutant protein was not identified in immortalized patient lymphocytes, indicating that it was likely unstable. The proband was a 57-year-old man with a lifelong history of chronic sinusitis and adult-onset recurrent pneumonia. His 80-year-old sister had an unremarkable medical history except for a severe Herpes zoster infection at age 70. Laboratory studies of both patients showed very low serum IgG and IgM, but normal mucosal IgA. Both individuals also had a severe and persistent B-cell lymphopenia and reduced numbers of class-switched memory B cells. Surface protein phenotyping of the B cells showed a developmental arrest after the transitional stage and before the cells became mature follicular B cells. In vitro functional expression studies showed that the mutant protein failed to bind BAFF (603969) and failed to induce downstream NFKB (164011) processing. Warnatz et al. (2009) emphasized the phenotypic differences in the patients, which suggested residual sufficient potential to develop B cells that can differentiate and provide host defense even in the absence of BAFFR function.

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

Last Updated: Oct 14, 2023