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NM_012186.3(FOXE3):c.92C>A (p.Pro31Gln) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 13, 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:
RCV002933513.3

Allele description

NM_012186.3(FOXE3):c.92C>A (p.Pro31Gln)

Genes:
FOXE3:forkhead box E3 [Gene - OMIM - HGNC]
LINC01389:long intergenic non-protein coding RNA 1389 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p33
Genomic location:
Preferred name:
NM_012186.3(FOXE3):c.92C>A (p.Pro31Gln)
HGVS:
  • NC_000001.11:g.47416407C>A
  • NG_016192.1:g.5336C>A
  • NM_012186.2:c.92C>A
  • NM_012186.3:c.92C>AMANE SELECT
  • NP_036318.1:p.Pro31Gln
  • NC_000001.10:g.47882079C>A
Protein change:
P31Q
Molecular consequence:
  • NM_012186.3:c.92C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Congenital primary aphakia
Synonyms:
ANTERIOR SEGMENT DYSGENESIS 2; Anterior segment dysgenesis 2, multiple subtypes
Identifiers:
MONDO: MONDO:0012456; MedGen: C1853230; Orphanet: 83461; OMIM: 610256
Name:
Anterior segment dysgenesis
Synonyms:
Ocular anterior segment dysgenesis
Identifiers:
MONDO: MONDO:0019503; MedGen: C1862839; OMIM: PS107250; Human Phenotype Ontology: HP:0007700

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003268008Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 13, 2023) 		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, SCV003268008.2

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

Description

This sequence change replaces proline, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 31 of the FOXE3 protein (p.Pro31Gln). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with FOXE3-related conditions. ClinVar contains an entry for this variant (Variation ID: 2059005). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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 16, 2024