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NM_014009.4(FOXP3):c.140G>T (p.Gly47Val) AND Insulin-dependent diabetes mellitus secretory diarrhea syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 19, 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:
RCV000699173.7

Allele description [Variation Report for NM_014009.4(FOXP3):c.140G>T (p.Gly47Val)]

NM_014009.4(FOXP3):c.140G>T (p.Gly47Val)

Gene:
FOXP3:forkhead box P3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.23
Genomic location:
Preferred name:
NM_014009.4(FOXP3):c.140G>T (p.Gly47Val)
HGVS:
  • NC_000023.11:g.49258366C>A
  • NG_007392.1:g.11466G>T
  • NM_001114377.2:c.140G>T
  • NM_014009.4:c.140G>TMANE SELECT
  • NP_001107849.1:p.Gly47Val
  • NP_054728.2:p.Gly47Val
  • NP_054728.2:p.Gly47Val
  • LRG_62t1:c.140G>T
  • LRG_62:g.11466G>T
  • LRG_62p1:p.Gly47Val
  • NC_000023.10:g.49114823C>A
  • NM_014009.3:c.140G>T
Protein change:
G47V
Links:
dbSNP: rs1432262933
NCBI 1000 Genomes Browser:
rs1432262933
Molecular consequence:
  • NM_001114377.2:c.140G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014009.4:c.140G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Insulin-dependent diabetes mellitus secretory diarrhea syndrome (IPEX)
Synonyms:
DIABETES MELLITUS, CONGENITAL INSULIN-DEPENDENT, WITH FATAL SECRETORY DIARRHEA; IMMUNODEFICIENCY, POLYENDOCRINOPATHY, AND ENTEROPATHY, X-LINKED; X-linked autoimmunity-allergic dysregulation syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010580; MedGen: C0342288; Orphanet: 37042; OMIM: 304790

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000827871Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 19, 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000827871.5

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

Description

The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 47 of the FOXP3 protein (p.Gly47Val). This variant has not been reported in the literature in individuals affected with FOXP3-related conditions. 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 sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 576632).

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

Last Updated: Feb 14, 2024