NM_052945.4(TNFRSF13C):c.485C>T (p.Pro162Leu) AND Immunodeficiency, common variable, 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 8, 2018
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:: RCV000816123.7

Allele description [Variation Report for NM_052945.4(TNFRSF13C):c.485C>T (p.Pro162Leu)]

NM_052945.4(TNFRSF13C):c.485C>T (p.Pro162Leu)

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.485C>T (p.Pro162Leu)

HGVS:

NC_000022.11:g.41925437G>A
NG_007579.1:g.6381C>T
NM_052945.4:c.485C>TMANE SELECT
NP_443177.1:p.Pro162Leu
NP_443177.1:p.Pro162Leu
LRG_184t1:c.485C>T
LRG_184:g.6381C>T
LRG_184p1:p.Pro162Leu
NC_000022.10:g.42321441G>A
NM_052945.3:c.485C>T

Protein change:

P162L

Links:

dbSNP: rs1602373110

NCBI 1000 Genomes Browser:

rs1602373110

Molecular consequence:

NM_052945.4:c.485C>T - 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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MAG: Sulfurovum sp. isolate MAG 30, whole genome shotgun sequencing project
MAG: Sulfurovum sp. isolate MAG 30, whole genome shotgun sequencing project
gi|1545589666|gb|QNZX00000000.1|QNZ 0000

Nucleotide
MAG: Alphaproteobacteria bacterium isolate MAG 149, whole genome shotgun sequenc...
MAG: Alphaproteobacteria bacterium isolate MAG 149, whole genome shotgun sequencing project
gi|1543922856|gb|QNXY00000000.1|QNX 0000

Nucleotide
MAG: Candidatus Thioglobus sp. isolate MAG 58, whole genome shotgun sequencing p...
MAG: Candidatus Thioglobus sp. isolate MAG 58, whole genome shotgun sequencing project
gi|1545603016|gb|QOAF00000000.1|QOA 0000

Nucleotide
beta-tubulin, partial [Talaromyces sp. ST-2024a]
beta-tubulin, partial [Talaromyces sp. ST-2024a]
gi|2813515558|gb|XHQ00159.1|

Protein
Aspergillus chevalieri isolate HGU11_3 internal transcribed spacer 1, partial se...
Aspergillus chevalieri isolate HGU11_3 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|2738858506|gb|PP860889.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000956615	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 8, 2018)	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

SCV000956615

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 8, 2018)

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, SCV000956615.4

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with TNFRSF13C-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with leucine at codon 162 of the TNFRSF13C protein (p.Pro162Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine.

#	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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