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NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg) AND Immunodeficiency, common variable, 2

Germline classification:
Conflicting interpretations of pathogenicity; risk factor (20 submissions)
Last evaluated:
Sep 22, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000005623.40

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]
Observations:
8

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000025805OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 2007)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000255489UCLA Clinical Genomics Center, UCLA - CES
criteria provided, single submitter

(Lee et al. (JAMA. 2014))
Likely pathogenic
(Jul 15, 2014)
germlineclinical testing

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

SCV000590895Center of Genomic medicine, Geneva, University Hospital of Geneva
criteria provided, single submitter

(ACMG Guidelines, 2015)
risk factor
(Jun 7, 2017)
maternalclinical testing

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

SCV000649856Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Jan 31, 2024)
germlineclinical testing

PubMed (11)
[See all records that cite these PMIDs]

SCV001427230Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Uncertain significance
(Mar 24, 2020)
germlineclinical testing

SCV001448757Knight Diagnostic Laboratories, Oregon Health and Sciences University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Sep 6, 2019)
germlineclinical testing

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

SCV001530692Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

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

SCV001837633Suma Genomics, Suma Genomics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significanceunknownclinical testing

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

SCV001934352Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 3, 2020)
unknownclinical testing

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

SCV001976896Laboratory of Medical Genetics, National & Kapodistrian University of Athens
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 6, 2021)
unknownclinical testing

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

SCV0020582453billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 3, 2022)
germlineclinical testing

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

PMID:21419480,

SCV002519879Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)
Pathogenic
(May 4, 2022)
germlineclinical testing

Citation Link,

SCV002568305Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Apr 26, 2022)
germlineclinical testing

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

SCV002759354Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Dec 7, 2022)
germlineclinical testing

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

SCV002764634Department of Pathology and Laboratory Medicine, Sinai Health System
no assertion criteria provided
Established risk alleleunknownresearch

SCV003807042Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
criteria provided, single submitter

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

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

SCV004046269Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

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

SCV005077735Institute of Immunology and Genetics Kaiserslautern
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 2, 2024)
germlineclinical testing

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

SCV005367966Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals
no assertion criteria provided

(ACMG Guidelines, 2015)
Pathogenic
(Aug 13, 2024)
maternalclinical testing

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

SCV005373927Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Sep 22, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes7not providednot provided7not providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedmaternalyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing, research
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

TACI is mutant in common variable immunodeficiency and IgA deficiency.

Castigli E, Wilson SA, Garibyan L, Rachid R, Bonilla F, Schneider L, Geha RS.

Nat Genet. 2005 Aug;37(8):829-34. Epub 2005 Jul 10.

PubMed [citation]
PMID:
16007086

Dominant-negative effect of the heterozygous C104R TACI mutation in common variable immunodeficiency (CVID).

Garibyan L, Lobito AA, Siegel RM, Call ME, Wucherpfennig KW, Geha RS.

J Clin Invest. 2007 Jun;117(6):1550-7. Epub 2007 May 10.

PubMed [citation]
PMID:
17492055
PMCID:
PMC1865037
See all PubMed Citations (15)

Details of each submission

From OMIM, SCV000025805.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a mother and son with common variable immunodeficiency-2 (240500), Castigli et al. (2005) identified a heterozygous 310T-C transition in exon 3 of the TNFRSF13B gene that resulted in a cys104-to-arg (C104R) substitution in the extracellular domain of TACI. Another unrelated woman with CVID2 was compound heterozygous for C104R and a single-basepair insertion (604907.0004). She inherited the C104R mutation from her father, who had selective immunoglobulin A deficiency-2 (609529), and transmitted the heterozygous C104R mutation to her son, who had CVID2. The proband's 2 sisters, who had IGAD2, were also heterozygous for the mutation. Heterozygosity for C104R was also found in 4 members of a third family with IGAD2. Studies of patient B cells showed that the mutant protein was expressed on the surface, but was unable to bind the ligand BAFF (603969); stimulation with APRIL (604472) failed to stimulate IgA or IgG secretion from B cells.

Salzer et al. (2005) identified the C104R mutation in affected members of a family with multiple cases of humoral immunodeficiency; 3 individuals who were heterozygous for the mutation had IGAD2, whereas 1 individuals who was homozygous for the mutation had CVID2. In addition, 2 unrelated patients with sporadic CVID were heterozygous for the mutation. Transformed B lymphocytes from patients showed severely compromised binding to APRIL and compromised B-cell proliferation; APRIL and BAFF failed to induce class-switch recombination in TACI-deficient B cells. Salzer et al. (2005) referred to the nucleotide substitution as 323T-C. The authors suggested that the incomplete penetrance of TACI mutations may reflect partial redundancy of the system.

Using in vitro transfection assays, Garibyan et al. (2007) showed that the C104R mutation, as well as its murine counterpart (C76R), interfered with TACI signaling in a dominant manner that was dependent on preassociation of C104R mutant TACI with wildtype TACI in the absence of ligand. Ligand was able to bind wildtype TACI, suggesting that C104R disrupts ligand-induced receptor rearrangement and signaling. These findings revealed that TACI preassembles as a homotypic oligomeric complex before binding ligand and provided a mechanism for how the heterozygous C104R mutation leads to CVID.

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

From UCLA Clinical Genomics Center, UCLA - CES, SCV000255489.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV000590895.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000649856.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (11)

Description

This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 104 of the TNFRSF13B protein (p.Cys104Arg). This variant is present in population databases (rs34557412, gnomAD 0.5%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with common variable immunodeficiency (CVID) (PMID: 16007087, 17392797, 19779048, 22697072, 24051380, 27123465). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5302). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TNFRSF13B protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects TNFRSF13B function (PMID: 16007087, 20889194, 21419480, 21458042, 23237420, 24051380). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

From Clinical Genomics Laboratory, Stanford Medicine, SCV001427230.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided

Description

The p.Cys104Arg variant in the TNFRSF13B gene has been previously reported in the heterozygous, compound heterozygous, or homozygous state in many individuals with common variable immunodeficiency (CVID; Castigli et al., 2005; de Valles-Ibáñez et al., 2018; Martinez-Polmar et al., 2009; Salzer et al., 2005). The p.Cys104Arg variant has also been identified in 697/129,190 European chromosomes, including 3 homozygotes, by the Genome Aggregation Database (http://gnomad.broadinstitute.org/), indicating it may be a common, reduced penetrance allele. The p.Cys104Arg variant is relatively common in the general population, and case-control studies provide conflicting evidence for an association with antibody deficiency (Castigli 2005; de VallesIbanez 2018; Pan-Hammarström et al, 2007; Pulvirenti et al., 2016; Salzer et al., 2009). Functional studies have shown that this variant impairs ligand binding, B cell proliferation, and antibody responses (Castigli et al., 2005; Fried et al., 2011; Lee et al., 2010; Salzer et al., 2005). Computational tools predict that the p.Cys104Arg variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Cys104Arg variant is uncertain; however, there is suspicion that this variant could be associated with common variable immunodeficiency due to functional studies and the predicted impact to the protein. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PS3_moderate; PP3]

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

From Knight Diagnostic Laboratories, Oregon Health and Sciences University, SCV001448757.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Baylor Genetics, SCV001530692.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Suma Genomics, Suma Genomics, SCV001837633.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001934352.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV001976896.1

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

Description

PM2, PM5, PP3, PP5

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

From 3billion, SCV002058245.1

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

Description

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000005302, PS1_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 21419480, 20889194, PS3_S). A different missense change at the same codon (p.Cys104Tyr) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000645207, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.919, 3CNET: 0.974, PP3_P). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

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

From Mendelics, SCV002519879.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV002568305.1

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

Description

PS3 PM1 PP3

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

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV002759354.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Department of Pathology and Laboratory Medicine, Sinai Health System, SCV002764634.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

The TNFRSF13B c.310T>C (p.Cys104Arg) variant has been reported in >50 homozygous, heterozygous, and compound heterozygous individuals with common variable immune deficiency (CVID), as well as in multiple healthy individuals (Salzer_2009_PMID: 18981294; Barroeta Seijas_2012_PMID: 22697072; Martinez-Gallo_2013_PMID: 23237420; Lee_2010_PMID: 20889194; Pulvirenti_2016_PMID: 27123465; Freiberger_2012_PMID: 22884984). In addition, this variant segregated with disease in at least 13 members from 7 families; however, asymptomatic homozygous and heterozygous family members were also identified, suggesting incomplete penetrance (Salzer_2009_PMID: 18981294; Barroeta Seijas_2012_PMID: 22697072; Martinez-Gallo_2013_PMID: 23237420; Koopmans_2013_PMID: 22983507). The variant was identified in dbSNP (ID: rs34557412) and ClinVar (classified as pathogenic by GeneDx and two other submitters, as likely pathogenic by Invitae and three other submitters, as uncertain significance by Laboratory for Molecular Medicine and five other submitters, as likely benign by Illumina and one other submitter, and as 'risk factor' by University Hospital of Geneva). The variant was identified in control databases in 983 of 282890 chromosomes (4 homozygous) at a frequency of 0.00347, and was observed at the highest frequency in the European (non-Finnish) population in 697 of 129190 chromosomes (freq: 0.005395) (Genome Aggregation Database March 6, 2019, v2.1.1). The p.C104 residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) suggest that the variant may impact the protein. Furthermore, multiple in vitro functional studies and murine models reveal that this variants leads to decreased protein surface expression, decreased antibody response, and impaired ligand binding ability compared to wildtype (Salzer_2009_PMID: 18981294; Martinez-Gallo_2013_PMID: 23237420; Lee_2010_PMID: 20889194; Bacchelli_2011_PMID: 21458042). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI) do not predict a deleterious effect on splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic - risk factor for common variable immunodeficiency.

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

From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV003807042.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
2not provided1not providednot providedclinical testing PubMed (1)
3not provided1not providednot providedclinical testing PubMed (1)
4not provided1not providednot providedclinical testing PubMed (1)
5not provided1not providednot providedclinical testing PubMed (1)
6not provided1not providednot providedclinical testing PubMed (1)

Description

ACMG classification criteria: PS3 supporting, PM3 moderated, PP1 moderated, PP3 supporting

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided
2germlineyes1not providednot provided1not providednot providednot provided
3germlineyes1not providednot provided1not providednot providednot provided
4germlineyes1not providednot provided1not providednot providednot provided
5germlineyes1not providednot provided1not providednot providednot provided
6germlineyes1not providednot provided1not providednot providednot provided

From Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV004046269.1

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

Description

This is a recurrent variant that has been reported as homozygous, compound heterozygous, and heterozygous change in individuals with common variable immunodeficiency (CVID) and in unaffected control individuals (PMID: 23237420, 17392797, 20156508, 24051380, 16007086, 16007087, 22884984). A study of 844 cases with CVID and 3924 controls found the p.Cys104Arg variant significantly enriched in cases versus controls (OR 5.60, CI 2.99-10.51, p=3.9 x 10-8) (PMID: 17392797). Further, a meta-analysis of 1,439 CVID patients and 3,558 controls confirmed enrichment of this variant in CVID cases versus controls (p < 10-5) (PMID: 22884984). In-vitro studies showed that the variant, which is located in the transmembrane (TM) domain of TACI, disrupts NF-kB/NF-AT signaling and leads to defective B-cell proliferation in response to stimulation (PMID: 21419480, 23237420, 19605846). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.35% (983/282890) and in the homozygote state in 4 individuals. The c.310T>C (p.Cys104Arg) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.310T>C (p.Cys104Arg) variant is classified as Likely Pathogenic.

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

From Institute of Immunology and Genetics Kaiserslautern, SCV005077735.1

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

Description

ACMG Criteria: PS3, PS4, PM1, PM3, PM5, PP1, PP3, PP5; Variant was found in heterozygous state

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

From Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals, SCV005367966.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV005373927.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024