NM_001006658.3(CR2):c.74C>G (p.Ser25Cys) AND Immunodeficiency, common variable, 7

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 13, 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:: RCV001359026.7

Allele description [Variation Report for NM_001006658.3(CR2):c.74C>G (p.Ser25Cys)]

NM_001006658.3(CR2):c.74C>G (p.Ser25Cys)

Gene:

CR2:complement C3d receptor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q32.2

Genomic location:

Preferred name:

NM_001006658.3(CR2):c.74C>G (p.Ser25Cys)

HGVS:

NC_000001.11:g.207466541C>G
NG_013006.1:g.17242C>G
NM_001006658.3:c.74C>GMANE SELECT
NM_001877.5:c.74C>G
NP_001006659.1:p.Ser25Cys
NP_001868.2:p.Ser25Cys
LRG_348:g.17242C>G
NC_000001.10:g.207639886C>G

Protein change:

S25C

Links:

dbSNP: rs1437268469

NCBI 1000 Genomes Browser:

rs1437268469

Molecular consequence:

NM_001006658.3:c.74C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001877.5:c.74C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Immunodeficiency, common variable, 7
Identifiers:: MONDO: MONDO:0013862; MedGen: C3542922; Orphanet: 1572; OMIM: 614699

Recent activity

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LOC129935141 [Homo sapiens]
LOC129935141 [Homo sapiens]
Gene ID:129935141

Gene
C18A3.7 Der GTPase-activating protein YihI [Caenorhabditis elegans]
C18A3.7 Der GTPase-activating protein YihI [Caenorhabditis elegans]
Gene ID:173972

Gene
nspc-14 Nematode Specific Peptide family, group C [Caenorhabditis elegans]
nspc-14 Nematode Specific Peptide family, group C [Caenorhabditis elegans]
Gene ID:181395

Gene
nspc-13 Nematode Specific Peptide family, group C [Caenorhabditis elegans]
nspc-13 Nematode Specific Peptide family, group C [Caenorhabditis elegans]
Gene ID:185671

Gene
dnj-28 J domain-containing protein [Caenorhabditis elegans]
dnj-28 J domain-containing protein [Caenorhabditis elegans]
Gene ID:171870

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001554886	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 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

SCV001554886

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 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, SCV001554886.4

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

Description

This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 25 of the CR2 protein (p.Ser25Cys). This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1051041). 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 disruptive. 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.

#	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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