ClinVar Miner

Submissions for variant NM_012452.2(TNFRSF13B):c.310T>C (p.Cys104Arg) (rs34557412)

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Total submissions: 18
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
UCLA Clinical Genomics Center, UCLA RCV000005623 SCV000255489 likely pathogenic Common variable immunodeficiency 2 2014-07-15 criteria provided, single submitter clinical testing
GeneDx RCV000403933 SCV000329550 pathogenic not provided 2018-10-02 criteria provided, single submitter clinical testing The C104R variant in the TNFRSF13B gene has been reported previously in association with both autosomal dominant and autosomal recessive forms of CVID and immunoglobulin A deficiency; however, this variant is most commonly associated with autosomal recessive inheritance (Salzer et al., 2009; Barroeta Seijas et al., 2012; Speletas et al., 2013; Martinez-Gallo et al., 2013; Lucena et al., 2015). Although an individual who was homozygous for the C104R variant has been reported to be clinically unaffected, his homozygous siblings had decreased immunoglobulin levels and were symptomatic (Martinez-Gallo et al., 2013). Functional studies have shown that the C104R variant is associated with impaired ligand binding and impaired B-cell function (Lee at al., 2010; Fried et al., 2011). Additionally, defective intracellular and extracellular expression of the gene is observed in individuals with CVID who are homozygous for the C104R variant, as well as in their clinically unaffected heterozygous relatives (Martinez-Gallo et al, 2013). The C104R variant is observed in 960/277246 (0.35%) alleles in large population cohorts, including 4 homozygotes (Lek et al., 2016). The C104R variant is a non-conservative amino acid substitution, which occurs at a position within the cysteine-rich domain 2, a region involved in disulfide bond formation (Hymowitz et al., 2005). We interpret C104R as a pathogenic variant.
Illumina Clinical Services Laboratory,Illumina RCV000302082 SCV000400917 likely benign Common Variable Immune Deficiency, Dominant 2016-06-14 criteria provided, single submitter clinical testing
Center of Genomic medicine, Geneva,University Hospital of Geneva RCV000005623 SCV000590895 risk factor Common variable immunodeficiency 2 2017-06-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001283708 SCV000605391 pathogenic none provided 2020-02-25 criteria provided, single submitter clinical testing The TNFRSF13B c.310T>C; p.Cys104Arg variant (rs34557412) has been reported in patients diagnosed with common variable immunodeficiency, and the association with the disease was found to be statistically significant (odds ratio 4.16 (1.98-8.74)) (Pan-Hammarstrom 2007). Additionally, functional studies show that this variant disrupts protein signaling (Martinez-Gallo 2013). However, this variant was also observed in clinically asymptomatic first-degree relatives and in up to 2.5% of unrelated healthy controls in certain ethnic populations (Pan-Hammarstrom 2007). This variant is reported in ClinVar (Variation ID: 5302), and is found in the general population with an overall allele frequency of 0.35% (983/282890 alleles, including 4 homozygotes) in the Genome Aggregation Database. Based on available information, this variant is considered to be a pathogenic CVID-associated variant with variable penetrance, that may act in co-existence with other genetic and/or environmental factors (Koopmans 2013). References: Koopmans et al. Clinical variability of family members with the C104R mutation in transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). J Clin Immunol. 2013 33(1):68-73. Martinez-Gallo et al. TACI mutations and impaired B-cell function in subjects with CVID and healthy heterozygotes. J Allergy Clin Immunol. 2013 131(2):468-476. Pan-Hammarstrom et al. Reexamining the role of TACI coding variants in common variable immunodeficiency and selective IgA deficiency. Nat Genet. 2007 39(4):429-30.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000403933 SCV000610665 likely benign not provided 2017-09-25 criteria provided, single submitter clinical testing
Invitae RCV000005623 SCV000649856 likely pathogenic Common variable immunodeficiency 2 2019-12-31 criteria provided, single submitter clinical testing This sequence change replaces cysteine with arginine at codon 104 of the TNFRSF13B protein (p.Cys104Arg). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and arginine. This variant is present in population databases (rs34557412, ExAC 0.5%). This variant has been reported in many individuals affected with common variable immunodeficiency (CVID) as homozygous, compound heterozygous with other TNFRSF13B variants, and as a heterozygous variant (PMID: 16007087, 17392797, 22697072, 27123465, 24051380, 19779048). This variant has also been seen as heterozygous in multiple unaffected relatives, but studies on B cells of these relatives show impaired function compared to unaffected individuals without TNFRSF13B variants (PMID: 23237420, 24051380). A meta-analysis of 1,423 CVID patients and 4,225 controls showed that this variant is significantly enriched in CVID patients (PMID: 22884984). In addition, this variant has been seen to segregate with disease in multiple families, although it appears to have reduced penetrance (PMID: 16007087, 19779048, 22983507, 22697072, 22884984, 23237420). The TNFRSF13B gene is also known as TACI in the literature. ClinVar contains an entry for this variant (Variation ID: 5302). Experimental studies have shown that this missense change disrupts ligand binding with APRIL, impairs B-cell proliferation in response to stimulation, and reduces the expression of TNFRSF13B on the surface of B-cells (PMID: 16007087, 21419480, 23237420). Individuals who are heterozygous for p.Cys104Arg have an increased number of autoreactive B-cells in the bone marrow (PMID: 24051380). In addition, mouse models with this variant also show reduced immunoglobulin production upon stimulation (PMID: 20889194, 21458042). In summary, this variant is a rare missense change that has been seen to segregate in multiple CVID families and disrupts protein function. This evidence indicates that the variant is pathogenic, but given the frequency of this variant in unaffected individuals, additional data is needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000403933 SCV000699342 uncertain significance not provided 2016-04-13 criteria provided, single submitter clinical testing Variant summary: The composite allele frequency of this variant is 1/309 in the general population. [Considering a recessive mode of inheritance, the maximal expected allele frequency of a disease-causing TNFRS13B allele is 1/418 (0.24%).] (Since there are other reported pathogenic TNFRS13B variants (e.g: pSer144X, p.Ser194Ter) that contribute to the disease, the observed allele frequency of 1/309 for the variant suggests that it is in the benign spectrum or is a low penetrance allele.) In families reported to carry this variant, there is no clear-cut inheritance pattern for it; however, recessive inheritance is supported by several studies. The dominant mode of inheritance is ruled out by high prevalence of the variant in controls as well as lack of cosegregation of this variant in dominant form in multiple reports (such as Poodt et al 2009). There are several reports that find the variant in compound heterozygousity as well as in homozygosity with CVID phenotype. In all compound heterozygous pts, second mutations inheritance (whether dominant or recessive mutation) can not been ascertained. However, there are also reports that subjects with this homozygous variant do not have CVID (Martnez-Pomar et al 2009) or do not fulfill diagnostic criteria for CVID (Koopmans et al 2013). These findings may suggest that this variant might be a recessive reduced penetrance mutation; however, the data are not clear enough. The functional data are suggestive of impaired activity of the variant; however, in lack of definitive genotype and phenotype data to support for pathogenicity, we cannot let functional data alone drive the variants pathogenicity. Martinez-Gallo et al 2013 showed that family members with the mutation in heterozygous or homozygous form, although not hypogammaglobulinemic, still have impaired B-cell TACI expression, reduced ligand binding, and markedly defective upregulation of AID mRNA, showing a dominantly inherited, selective in vitro activation defect. The authors conclude that, B cells of relatives of subjects with CVID who have mutations in TACI but normal immune globulin levels still have detectable in vitro B-cell defects. Moreover, Romberg et al 2013 also conclude that this mutation may favor CVID by altering B cell activation with coincident impairment of central B cell tolerance.Some case-control studies show that this variant might be associated with increased disease risk; however, odds ratios are not high to derive a definitive conclusion. Freiberger et al 2012 concludes, The p.C104R and p.A181E mutations and premature stop codon introducing mutations appear to be relevant, either alone or more likely in combination with other genetic and/or environmental factor(s), although statistically significant association was only demonstrated with CVID for the p.C104R, p.A181E and p.L69TfsX12 mutations, mainly because other protein truncating mutations are very rare.Taken together, due to some conflicts and uncertainties in literature about the variants pathogenicity, a classification of VUS is appropriate at this time.
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles RCV000735370 SCV000854523 uncertain significance Clubfoot; Skeletal dysplasia; Micrognathia; Hemivertebrae; Preaxial foot polydactyly; Respiratory failure; Short femur; Vertebral segmentation defect; Pseudoarthrosis; Chronic lung disease; Interstitial pulmonary abnormality; Coat hanger sign of ribs; Vertebral hypoplasia; Absent epiphyses; Cleft palate; Patent ductus arteriosus criteria provided, single submitter clinical testing
Blueprint Genetics RCV000403933 SCV000927312 uncertain significance not provided 2017-06-26 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000507544 SCV000966775 uncertain significance not specified 2018-07-27 criteria provided, single submitter clinical testing proposed classification - variant undergoing re-assessment, contact laboratory
CeGaT Praxis fuer Humangenetik Tuebingen RCV000403933 SCV001250126 pathogenic not provided 2020-12-01 criteria provided, single submitter clinical testing
Knight Diagnostic Laboratories, Oregon Health and Sciences University RCV000005623 SCV001448757 likely pathogenic Common variable immunodeficiency 2 2019-09-06 criteria provided, single submitter clinical testing
Baylor Genetics RCV000005623 SCV001530692 uncertain significance Common variable immunodeficiency 2 2018-06-18 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
OMIM RCV000005623 SCV000025805 pathogenic Common variable immunodeficiency 2 2007-06-01 no assertion criteria provided literature only
OMIM RCV000005624 SCV000025806 pathogenic Immunoglobulin A deficiency 2 2007-06-01 no assertion criteria provided literature only
Clinical Genomics Program, Stanford Medicine RCV000005623 SCV001427230 uncertain significance Common variable immunodeficiency 2 2020-03-24 no assertion criteria provided clinical testing 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 (, 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]
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn RCV001374734 SCV001571337 likely pathogenic Severe SARS-CoV-2 infection, susceptibility to 2021-03-03 no assertion criteria provided clinical testing This variant was observed in homozygous state in a child with a lethal course of covid-19. The child was also homozygous for a splice site variant in TBK1, that is associated to autoinflammatory disorder. Probably a combination of the deleterious homozygous missense mutation in TNFRSF13B and the homozygous splice site mutation in TBK1 in the presence of an autoinflammatory disease and its treatment regimen - might have promoted the severe disease course observed in the present case either alone or in concert.

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