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NM_012186.3(FOXE3):c.232G>A (p.Ala78Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: May 11, 2021)
Last evaluated:
May 20, 2019
Accession:
VCV000427852.3
Variation ID:
427852
Description:
single nucleotide variant
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NM_012186.3(FOXE3):c.232G>A (p.Ala78Thr)

Allele ID
418809
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p33
Genomic location
1: 47416547 (GRCh38) GRCh38 UCSC
1: 47882219 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.47882219G>A
NC_000001.11:g.47416547G>A
NM_012186.3:c.232G>A MANE Select NP_036318.1:p.Ala78Thr missense
NG_016192.1:g.5476G>A
Protein change
A78T
Other names
-
Canonical SPDI
NC_000001.11:47416546:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00007
Exome Aggregation Consortium (ExAC) 0.00007
The Genome Aggregation Database (gnomAD), exomes 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00011
Links
ClinGen: CA842917
dbSNP: rs377669670
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, single submitter Jun 1, 2017 RCV000521849.2
Uncertain significance 1 criteria provided, single submitter May 20, 2019 RCV001062090.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FOXE3 No evidence available No evidence available GRCh38
GRCh37
- 140
LINC01389 - - - GRCh38 - 132

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 01, 2017)
criteria provided, single submitter
Method: clinical testing
Congenital primary aphakia
(Autosomal recessive inheritance)
Allele origin: germline
Genetics Department, University Hospital of Toulouse
Accession: SCV000579340.1
Submitted: (Jun 13, 2017)
Evidence details
Uncertain significance
(May 20, 2019)
criteria provided, single submitter
Method: clinical testing
Anterior segment dysgenesis
Congenital primary aphakia
Allele origin: germline
Invitae
Accession: SCV001226866.1
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces alanine with threonine at codon 78 of the FOXE3 protein (p.Ala78Thr). The alanine residue is moderately conserved and there is a … (more)
Pathogenic
(May 01, 2021)
no assertion criteria provided
Method: research
Congenital primary aphakia
Allele origin: germline
Human Developmental Genetics Laboratory,Medical College of Wisconsin
Accession: SCV001593178.1
Submitted: (May 11, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
FOXE3 mutations: genotype-phenotype correlations. Plaisancié J Clinical genetics 2018 PMID: 29136273

Text-mined citations for rs377669670...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021