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NM_000448.3(RAG1):c.1559T>C (p.Phe520Ser) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 26, 2022
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:
RCV000795118.8

Allele description [Variation Report for NM_000448.3(RAG1):c.1559T>C (p.Phe520Ser)]

NM_000448.3(RAG1):c.1559T>C (p.Phe520Ser)

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.1559T>C (p.Phe520Ser)
HGVS:
  • NC_000011.10:g.36574863T>C
  • NG_007528.1:g.11851T>C
  • NM_000448.3:c.1559T>CMANE SELECT
  • NM_001377277.1:c.1559T>C
  • NM_001377278.1:c.1559T>C
  • NM_001377279.1:c.1559T>C
  • NM_001377280.1:c.1559T>C
  • NP_000439.1:p.Phe520Ser
  • NP_000439.2:p.Phe520Ser
  • NP_001364206.1:p.Phe520Ser
  • NP_001364207.1:p.Phe520Ser
  • NP_001364208.1:p.Phe520Ser
  • NP_001364209.1:p.Phe520Ser
  • LRG_98t1:c.1559T>C
  • LRG_98:g.11851T>C
  • LRG_98p1:p.Phe520Ser
  • NC_000011.9:g.36596413T>C
  • NM_000448.2:c.1559T>C
Protein change:
F520S
Links:
dbSNP: rs1490273597
NCBI 1000 Genomes Browser:
rs1490273597
Molecular consequence:
  • NM_000448.3:c.1559T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377277.1:c.1559T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377278.1:c.1559T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377279.1:c.1559T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377280.1:c.1559T>C - 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
Name:
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive
Synonyms:
SCID, T CELL-NEGATIVE, B CELL-NEGATIVE, NK CELL-POSITIVE; Severe immunodeficiency, autosomal recessive, T-cell negative, B-cell negative, NK cell-positive; SCID, AR, T-cell negative, B-cell negative, NK cell-positive; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011086; MedGen: C1832322; Orphanet: 331206; OMIM: 601457

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000934560Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 26, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV000934560.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces phenylalanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 520 of the RAG1 protein (p.Phe520Ser). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with RAG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 641796). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RAG1 protein function. 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.

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

Last Updated: Sep 29, 2024