NM_052945.4(TNFRSF13C):c.289G>A (p.Gly97Ser) AND Immunodeficiency, common variable, 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 18, 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:: RCV003611251.3

Allele description [Variation Report for NM_052945.4(TNFRSF13C):c.289G>A (p.Gly97Ser)]

NM_052945.4(TNFRSF13C):c.289G>A (p.Gly97Ser)

Genes:

LOC130067574:ATAC-STARR-seq lymphoblastoid silent region 13813 [Gene]
TNFRSF13C:TNF receptor superfamily member 13C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.2

Genomic location:

Preferred name:

NM_052945.4(TNFRSF13C):c.289G>A (p.Gly97Ser)

HGVS:

NC_000022.11:g.41926179C>T
NG_007579.1:g.5639G>A
NG_201989.1:g.153C>T
NM_052945.4:c.289G>AMANE SELECT
NP_443177.1:p.Gly97Ser
NP_443177.1:p.Gly97Ser
LRG_184t1:c.289G>A
LRG_184:g.5639G>A
LRG_184p1:p.Gly97Ser
NC_000022.10:g.42322183C>T
NM_052945.3:c.289G>A

Protein change:

G97S

Molecular consequence:

NM_052945.4:c.289G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Immunodeficiency, common variable, 4
Synonyms:: ANTIBODY DEFICIENCY DUE TO BAFFR DEFECT
Identifiers:: MONDO: MONDO:0013284; MedGen: C3150739; Orphanet: 1572; OMIM: 613494

Recent activity

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Makaira indica mitochondrion, complete genome
Makaira indica mitochondrion, complete genome
gi|229918831|ref|NC_012675.1|

Nucleotide
ornithine decarboxylase, partial [Saltator atricollis]
ornithine decarboxylase, partial [Saltator atricollis]
gi|315488304|gb|ADU32787.1|

Protein
Istiompax indica voucher AWFS-F16-0211 large subunit ribosomal RNA gene, partial...
Istiompax indica voucher AWFS-F16-0211 large subunit ribosomal RNA gene, partial sequence; mitochondrial
gi|1743541600|gb|MN473671.1|

Nucleotide
Istiompax indica NSTP:DNA 17116 mitochondrial gene for 12S rRNA, partial sequenc...
Istiompax indica NSTP:DNA 17116 mitochondrial gene for 12S rRNA, partial sequence
gi|1918447926|dbj|LC579328.1|

Nucleotide
Istiompax indica isolate Vizh_IstI2 cytochrome c oxidase subunit I (COX1) gene, ...
Istiompax indica isolate Vizh_IstI2 cytochrome c oxidase subunit I (COX1) gene, partial cds; mitochondrial
gi|2069256818|gb|MZ572970.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004481699	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004481699

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 18, 2023)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004481699.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. This variant has not been reported in the literature in individuals affected with TNFRSF13C-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 97 of the TNFRSF13C protein (p.Gly97Ser).

#	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: Sep 29, 2024

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