VCV000568112.2 - ClinVar

NM_001453.3(FOXC1):c.1_*1790del (p.Met1fs)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001453.3(FOXC1):c.1_*1790del (p.Met1fs)

Variation ID: 568112 Accession: VCV000568112.2

Type and length

Deletion, 3,452 bp

Location

Cytogenetic: 6p25.3 6: 1610446-1613897 (GRCh38) [ NCBI UCSC ] 6: 1610681-1614132 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 10, 2018	Sep 3, 2023	Mar 22, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_001453.3:c.1_*1790del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001444.2:p.Met1fs	frameshift initiator codon variant
NC_000006.12:g.1610446_1613897del
NC_000006.11:g.1610681_1614132del
NG_009368.1:g.5001_8452del
LRG_1245:g.5001_8452del
LRG_1245t1:c.1_*1790del	LRG_1245p1:p.Met1fs

... more HGVS ... less HGVS

Protein change

M1fs

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
FOXC1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	534	675
LOC129995601	-	-	-	GRCh38	-	84

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Axenfeld-Rieger syndrome type 3	Pathogenic (1)	criteria provided, single submitter	Mar 22, 2018	RCV000688364.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Mar 22, 2018)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Axenfeld-Rieger syndrome type 3 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000815972.2 First in ClinVar: Oct 10, 2018 Last updated: Sep 03, 2023	Publications: PubMed (3) PubMed: 28492532‚ 20881294‚ 22382802 Comment: This sequence change is a complex rearrangement involving exon 1 of the FOXC1 mRNA (c.-4362-878delins261). This removes the initiator methionine along with approximately half of … (more) This sequence change is a complex rearrangement involving exon 1 of the FOXC1 mRNA (c.-4362-878delins261). This removes the initiator methionine along with approximately half of the coding sequence and over 4kb of upstream sequence. As such, this likely results in the absence of a FOXC1 protein product. While this particular variant has not been reported in the literature, deletion of the entire FOXC1 gene has been reported in several individuals affected with anterior segment dysgenesis and Axenfeld-Rieger syndrome (PMID: 20881294, 22382802). Loss-of-function variants in FOXC1 are known to be pathogenic (PMID: 16936096, 20881294). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This sequence change is a complex rearrangement involving exon 1 of the FOXC1 mRNA (c.-4362-878delins261). This removes the initiator methionine along with approximately half of the coding sequence and over 4kb of upstream sequence. As such, this likely results in the absence of a FOXC1 protein product. While this particular variant has not been reported in the literature, deletion of the entire FOXC1 gene has been reported in several individuals affected with anterior segment dysgenesis and Axenfeld-Rieger syndrome (PMID: 20881294, 22382802). Loss-of-function variants in FOXC1 are known to be pathogenic (PMID: 16936096, 20881294). For these reasons, this variant has been classified as Pathogenic.

Germline Functional Evidence

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Exon-level array CGH in a large clinical cohort demonstrates increased sensitivity of diagnostic testing for Mendelian disorders.	Aradhya S	Genetics in medicine : official journal of the American College of Medical Genetics	2012	PMID: 22382802
Expanding the spectrum of FOXC1 and PITX2 mutations and copy number changes in patients with anterior segment malformations.	D'haene B	Investigative ophthalmology & visual science	2011	PMID: 20881294

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_001453.3(FOXC1):c.1_*1790del (p.Met1fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...