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NM_000448.3(RAG1):c.1566G>T (p.Trp522Cys) AND Combined immunodeficiency with skin granulomas

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Oct 2, 2015
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000022745.19

Allele description [Variation Report for NM_000448.3(RAG1):c.1566G>T (p.Trp522Cys)]

NM_000448.3(RAG1):c.1566G>T (p.Trp522Cys)

Gene:
RAG1:recombination activating 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p12
Genomic location:
Preferred name:
NM_000448.3(RAG1):c.1566G>T (p.Trp522Cys)
HGVS:
  • NC_000011.10:g.36574870G>T
  • NG_007528.1:g.11858G>T
  • NM_000448.3:c.1566G>TMANE SELECT
  • NM_001377277.1:c.1566G>T
  • NM_001377278.1:c.1566G>T
  • NM_001377279.1:c.1566G>T
  • NM_001377280.1:c.1566G>T
  • NP_000439.1:p.Trp522Cys
  • NP_000439.2:p.Trp522Cys
  • NP_001364206.1:p.Trp522Cys
  • NP_001364207.1:p.Trp522Cys
  • NP_001364208.1:p.Trp522Cys
  • NP_001364209.1:p.Trp522Cys
  • LRG_98t1:c.1566G>T
  • LRG_98:g.11858G>T
  • LRG_98p1:p.Trp522Cys
  • NC_000011.9:g.36596420G>T
  • NM_000448.2:c.1566G>T
  • P15918:p.Trp522Cys
Protein change:
W522C; TRP522CYS
Links:
UniProtKB: P15918#VAR_025980; OMIM: 179615.0024; dbSNP: rs193922461
NCBI 1000 Genomes Browser:
rs193922461
Molecular consequence:
  • NM_000448.3:c.1566G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377277.1:c.1566G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377278.1:c.1566G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377279.1:c.1566G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377280.1:c.1566G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Combined immunodeficiency with skin granulomas
Synonyms:
Combined cellular and humoral immune defects with granulomas
Identifiers:
MONDO: MONDO:0009306; MedGen: C2673536; OMIM: 233650

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000044034OMIM
no assertion criteria provided
Pathogenic
(Aug 26, 2010)
germlineliterature only

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

SCV000053058Women's Health and Genetics/Laboratory Corporation of America, LabCorp
no assertion criteria provided
Likely pathogenic
(Oct 2, 2015)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Hypomorphic Rag mutations can cause destructive midline granulomatous disease.

De Ravin SS, Cowen EW, Zarember KA, Whiting-Theobald NL, Kuhns DB, Sandler NG, Douek DC, Pittaluga S, Poliani PL, Lee YN, Notarangelo LD, Wang L, Alt FW, Kang EM, Milner JD, Niemela JE, Fontana-Penn M, Sinal SH, Malech HL.

Blood. 2010 Aug 26;116(8):1263-71. doi: 10.1182/blood-2010-02-267583. Epub 2010 May 20.

PubMed [citation]
PMID:
20489056
PMCID:
PMC2938237

Details of each submission

From OMIM, SCV000044034.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a boy with destructive midline granulomatous disease of the head and neck (CCHIDG; 233650), De Ravin et al. (2010) identified compound heterozygosity for 2 mutations in the RAG1 gene: a 1566G-T transversion, resulting in a trp522-to-cys (W522C) substitution, and a 1-bp deletion (1621delC; 179615.0025), resulting in a frameshift and premature termination after 30 novel residues. Each unaffected parent was heterozygous for 1 of the mutations. The patient had a complicated medical history. He had a history of myasthenia gravis with thymectomy at age 10 years, and a history of recurrent ear and sinus infections. The thymus showed dysplastic features and absence of autoimmune regulator, indicating a defect in thymocyte maturation. Laboratory studies showed a decrease of IgG subclasses 2 and 4 and mild CD8+ T cell lymphopenia, whereas CD3+ T cells, CD19+ B cells, and NK cells were normal. He was treated for Wegener granulomatosis with chemotherapeutic agents, but developed severe lymphopenia and continued to have relapses of noninfectious granulomas. In vitro studies showed dysregulated cellular inflammatory responses to various stimuli, including increased production of IL1B (147720) and IL8 (146930). Functional studies showed that the W522C mutant had about 50% residual RAG1 activity, but the deletion mutation had no activity. An older sister had autoimmune cytopenias and antinuclear antibody-positive collagen vascular disease, with death at age 5 years. De Ravin et al. (2010) concluded that the proband had a phenotypic variant of RAG1 deficiency, with some residual enzyme activity being responsible for the later presentation and milder phenotype. The authors suggested a dysregulation of the inflammatory response to environmental antigens in this patient.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000053058.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1566G>T (p.Trp522Cys) variant involves the alteration of a conserved nucleotide and 4/4 in silico tools predict a pathogenic outcome. The variant is present at a low frequency in the control population (0.01% in ExAC), but has been reported in the literature in patients with granulomatous disease (De Ravin_2010), atypical SCID/OS (Villa_2000, Kwan_2013) and common variable immunodeficiency (Lee_2014, Buchbinder_2014). In vitro analysis showed the variant to result in recombination acitivty that was 50-60% reduced compared to WT (De Ravin_2010, Lee_2014).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024