rs72553877
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PP3PP5
The NM_012452.3(TNFRSF13B):c.260T>A(p.Ile87Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000478 in 1,614,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00035 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00049 ( 0 hom. )
Consequence
TNFRSF13B
NM_012452.3 missense
NM_012452.3 missense
Scores
4
5
6
Clinical Significance
Conservation
PhyloP100: 4.18
Genes affected
TNFRSF13B (HGNC:18153): (TNF receptor superfamily member 13B) The protein encoded by this gene is a lymphocyte-specific member of the tumor necrosis factor (TNF) receptor superfamily. It interacts with calcium-modulator and cyclophilin ligand (CAML). The protein induces activation of the transcription factors NFAT, AP1, and NF-kappa-B and plays a crucial role in humoral immunity by interacting with a TNF ligand. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM1
?
In a repeat TNFR-Cys 2 (size 34) in uniprot entity TR13B_HUMAN there are 8 pathogenic changes around while only 3 benign (73%) in NM_012452.3
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.797
PP5
?
Variant 17-16948923-A-T is Pathogenic according to our data. Variant chr17-16948923-A-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 618436.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=2, Likely_pathogenic=3, not_provided=1, Uncertain_significance=2}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF13B | NM_012452.3 | c.260T>A | p.Ile87Asn | missense_variant | 3/5 | ENST00000261652.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF13B | ENST00000261652.7 | c.260T>A | p.Ile87Asn | missense_variant | 3/5 | 1 | NM_012452.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000348 AC: 53AN: 152210Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000457 AC: 115AN: 251460Hom.: 0 AF XY: 0.000449 AC XY: 61AN XY: 135902
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GnomAD4 exome AF: 0.000491 AC: 718AN: 1461876Hom.: 0 Cov.: 35 AF XY: 0.000488 AC XY: 355AN XY: 727238
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GnomAD4 genome ? AF: 0.000348 AC: 53AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74500
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:6Uncertain:2Other:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Pathogenic:2Uncertain:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 13, 2023 | Reported as a single heterozygous variant in patients with common variable immune deficiency or selective IgA deficiency in the published literature, as well as in unaffected individuals (Barroeta Seijas et al., 2012; Chase et al., 2013; Pulvirenti et al., 2016); Published functional studies demonstrate no effect on cell surface expression, but a significant reduction in signaling (Fried et al., 2011); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21041728, 34975878, 23956760, 17697196, 18981294, 21850030, 22884984, 22627058, 21419480, 19494827, 21458042, 19629655, 28554560, 22697072, 22930256, 27123465, 30269248, 30290665, 31681265, 34426522, 31589614, 35686370, 34573280, 32581362, 34441032) - |
Likely pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 31, 2017 | The p.Ile87Asn variant (rs72553877) has been reported in the heterozygous and compound heterozygous state in multiple families and individuals diagnosed with common variable immunodeficiency (CVID), asthma, or lymphoproliferative disorders (Freiberger 2012, Janzi 2012, Lougaris 2012, Salzer 2009, and Speletas 2013). This variant has also been observed by our laboratory in a patient who inherited the variant from his unaffected father and was reported to have chronic infections and IgA deficiency. Functional evidence demonstrates that the p.Ile87Asn variant causes a defect in ligand binding as well as reduced activation of NFkB signaling (Fried 2011, Lougaris 2012, and Salzer 2009). The p.Ile87Asn variant is also listed in the Genome Aggregation Database (gnomAD) browser with an allele frequency of 0.068% in the non-Finnish European population (identified in 86 out of 126,692 chromosomes), but was not detected in the homozygous state. The isoleucine at codon 87 is moderately conserved considering 10 species (Alamut software v2.10.0), and computational analyses predict that this variant does affect the structure/function of the TNFRSF13B protein (SIFT: damaging, PolyPhen2: probably damaging, MutationTaster: disease causing). Therefore, based on the available evidence, the p.Ile87Asn variant is classified as likely pathogenic. - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | TNFRSF13B: PS4:Moderate, PP1, PS3:Supporting - |
Uncertain significance, criteria provided, single submitter | clinical testing | Blueprint Genetics | Mar 19, 2019 | - - |
Immunodeficiency, common variable, 2 Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | This sequence change replaces isoleucine, which is neutral and non-polar, with asparagine, which is neutral and polar, at codon 87 of the TNFRSF13B protein (p.Ile87Asn). This variant is present in population databases (rs72553877, gnomAD 0.07%). This missense change has been observed in individual(s) with common variable immunodeficiency (CVID) (PMID: 22627058, 22697072, 22884984, 27123465, 30290665, 31681265). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 618436). 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: 21419480, 21458042). For these reasons, this variant has been classified as Pathogenic. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Clinic of Clinical Immunology with Stem Cell Bank, Expert Centre for Rare Diseases - PID, University Hospital "Alexandrovska" | - | - - |
Common variable immunodeficiency Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 15, 2022 | Variant summary: TNFRSF13B c.260T>A (p.Ile87Asn) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00046 in 254886 control chromosomes. c.260T>A has been reported in the literature in individuals affected with Common Variable Immunodeficiency (e.g. Bacchelli_2007, Pan-Hammarstrom_2008, PanSalzer_2009, Lougaris_2012, Rojas-Restrepo_2021). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and showed that this variant resulted in decreased activity (Salzer_2009, Fried_2011, Lougaris_2012). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (pathogenic/likely pathogenic n=3, VUS n=2). Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
IgAD1;C3150354:Immunodeficiency, common variable, 2 Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant classified as Pathogenic and reported on 06-12-2021 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Benign
Dann
Benign
DEOGEN2
Uncertain
D;D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Pathogenic
D
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
Sift4G
Pathogenic
D;D;D
Polyphen
0.99, 0.98
.;D;D
Vest4
MVP
MPC
0.077
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at