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NM_000538.4(RFXAP):c.175G>A (p.Ala59Thr) AND MHC class II deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 4, 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:
RCV001037809.7

Allele description

NM_000538.4(RFXAP):c.175G>A (p.Ala59Thr)

Gene:
RFXAP:regulatory factor X associated protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q13.3
Genomic location:
Preferred name:
NM_000538.4(RFXAP):c.175G>A (p.Ala59Thr)
HGVS:
  • NC_000013.11:g.36819532G>A
  • NG_007876.1:g.5331G>A
  • NM_000538.4:c.175G>AMANE SELECT
  • NP_000529.1:p.Ala59Thr
  • LRG_103t1:c.175G>A
  • LRG_103:g.5331G>A
  • NC_000013.10:g.37393669G>A
  • NM_000538.3:c.175G>A
Protein change:
A59T
Links:
dbSNP: rs867140153
NCBI 1000 Genomes Browser:
rs867140153
Molecular consequence:
  • NM_000538.4:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
MHC class II deficiency
Synonyms:
BLS, TYPE II; SCID, HLA CLASS II-NEGATIVE; Bare Lymphocyte Syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008855; MedGen: C2931418; Orphanet: 572; OMIM: PS209920

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001201241Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 4, 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 Invitae, SCV001201241.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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 tolerated. ClinVar contains an entry for this variant (Variation ID: 836633). This variant has not been reported in the literature in individuals affected with RFXAP-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 59 of the RFXAP protein (p.Ala59Thr).

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

Last Updated: Jun 2, 2024