NM_001006658.3(CR2):c.424C>T (p.Arg142Ter) AND Immunodeficiency, common variable, 7

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 22, 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:: RCV000650308.8

Allele description [Variation Report for NM_001006658.3(CR2):c.424C>T (p.Arg142Ter)]

NM_001006658.3(CR2):c.424C>T (p.Arg142Ter)

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.424C>T (p.Arg142Ter)

HGVS:

NC_000001.11:g.207466891C>T
NG_013006.1:g.17592C>T
NM_001006658.3:c.424C>TMANE SELECT
NM_001877.5:c.424C>T
NP_001006659.1:p.Arg142Ter
NP_001006659.1:p.Arg142Ter
NP_001868.2:p.Arg142Ter
LRG_348t1:c.424C>T
LRG_348:g.17592C>T
LRG_348p1:p.Arg142Ter
NC_000001.10:g.207640236C>T
NM_001006658.2:c.424C>T

Protein change:

R142*

Links:

dbSNP: rs201017642

NCBI 1000 Genomes Browser:

rs201017642

Molecular consequence:

NM_001006658.3:c.424C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001877.5:c.424C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Mycobacterium sp. BK086 Ga0307707_102, whole genome shotgun sequence
Mycobacterium sp. BK086 Ga0307707_102, whole genome shotgun sequence
gi|1598053161|ref|NZ_SNWL01000004.1 |WGS:NZ_SNWL01|Ga0307707_102

Nucleotide
Y51A2B.6 protein of unknown function WSN domain-containing protein [Caenorhabdit...
Y51A2B.6 protein of unknown function WSN domain-containing protein [Caenorhabditis elegans]
Gene ID:190131

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000772149	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 22, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 28499783, 26325596, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000772149

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 22, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

CD21 deficiency in 2 siblings with recurrent respiratory infections and hypogammaglobulinemia.

Rosain J, Miot C, Lambert N, Rousselet MC, Pellier I, Picard C.

J Allergy Clin Immunol Pract. 2017 Nov - Dec;5(6):1765-1767.e3. doi: 10.1016/j.jaip.2017.04.011. Epub 2017 May 10. No abstract available.

PubMed [citation]

PMID:: 28499783

CD21 and CD19 deficiency: Two defects in the same complex leading to different disease modalities.

Wentink MW, Lambeck AJ, van Zelm MC, Simons E, van Dongen JJ, IJspeert H, Schölvinck EH, van der Burg M.

Clin Immunol. 2015 Dec;161(2):120-7. doi: 10.1016/j.clim.2015.08.010. Epub 2015 Aug 30.

PubMed [citation]

PMID:: 26325596

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000772149.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Arg142*) in the CR2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CR2 are known to be pathogenic (PMID: 26325596, 28499783). This variant is present in population databases (rs201017642, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with hypogammaglobulinemia (PMID: 26325596). ClinVar contains an entry for this variant (Variation ID: 540314). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#	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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