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NM_001453.3(FOXC1):c.404G>A (p.Cys135Tyr) AND FOXC1-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 14, 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:
RCV003399860.4

Allele description [Variation Report for NM_001453.3(FOXC1):c.404G>A (p.Cys135Tyr)]

NM_001453.3(FOXC1):c.404G>A (p.Cys135Tyr)

Gene:
FOXC1:forkhead box C1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p25.3
Genomic location:
Preferred name:
NM_001453.3(FOXC1):c.404G>A (p.Cys135Tyr)
HGVS:
  • NC_000006.12:g.1610849G>A
  • NG_009368.1:g.5404G>A
  • NG_175047.1:g.277G>A
  • NM_001453.3:c.404G>AMANE SELECT
  • NP_001444.2:p.Cys135Tyr
  • LRG_1245t1:c.404G>A
  • LRG_1245:g.5404G>A
  • LRG_1245p1:p.Cys135Tyr
  • NC_000006.11:g.1611084G>A
  • NM_001453.2:c.404G>A
Protein change:
C135Y
Molecular consequence:
  • NM_001453.3:c.404G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
FOXC1-related disorder
Synonyms:
FOXC1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004110430PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Dec 14, 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004110430.1

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

Description

The FOXC1 c.404G>A variant is predicted to result in the amino acid substitution p.Cys135Tyr. This variant was reported as de novo in an individual with bilateral congenital glaucoma (Chakrabarti et al. 2009. PubMed ID: 18708620). Functional studies found this variant did not localize to the nucleus as efficiently and was unable to bind DNA compared to wild type FOXC1 (Seifi et al. 2016. PubMed ID: 27804176). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as likely pathogenic.

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

Last Updated: May 12, 2024