VCV002952719.1 - ClinVar

NM_001110556.2(FLNA):c.6395_6396del (p.Val2132fs)

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.

(2)

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, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001110556.2(FLNA):c.6395_6396del (p.Val2132fs)

Variation ID: 2952719 Accession: VCV002952719.1

Type and length

Microsatellite, 2 bp

Location

Cytogenetic: Xq28 X: 154352659-154352660 (GRCh38) [ NCBI UCSC ] X: 153581027-153581028 (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	Feb 29, 2024	Apr 15, 2024	Jan 15, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001110556.2:c.6395_6396del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001104026.1:p.Val2132fs	frameshift
NM_001456.3:c.6371_6372del
NM_001456.4:c.6371_6372del	NP_001447.2:p.Val2124fs	frameshift
NC_000023.11:g.154352659CA[1]
NC_000023.10:g.153581027CA[1]
NG_011506.2:g.26977TG[1]
LRG_1340:g.26977TG[1]
LRG_1340t1:c.6395_6396del	LRG_1340p1:p.Val2132fs

... more HGVS ... less HGVS

Protein change

V2132fs, V2124fs

Other names

Canonical SPDI

NC_000023.11:154352658:CACA:CA

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.
FLNA		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	3151	3592

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.
Frontometaphyseal dysplasia Heterotopia, periventricular, X-linked dominant Melnick-Needles syndrome Oto-palato-digital syndrome, type II	Pathogenic (1)	criteria provided, single submitter	Jan 15, 2024	RCV003817853.2
Heterotopia, periventricular, X-linked dominant	Pathogenic (1)	criteria provided, single submitter	Jun 26, 2018	RCV003992796.1

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 (Jan 15, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Oto-palato-digital syndrome, type II Heterotopia, periventricular, X-linked dominant Frontometaphyseal dysplasia Melnick-Needles syndrome Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004607306.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Publications: PubMed (3) PubMed: 16684786‚ 20730588‚ 26471271 Comment: This sequence change creates a premature translational stop signal (p.Val2124Glufs26) in the FLNA gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Val2124Glufs26) in the FLNA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FLNA are known to be pathogenic (PMID: 16684786, 20730588, 26471271). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FLNA-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)
Pathogenic (Jun 26, 2018)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Heterotopia, periventricular, X-linked dominant (X-linked dominant inheritance) Affected status: yes Allele origin: de novo	Institute of Human Genetics, University of Leipzig Medical Center Accession: SCV004812160.1 First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024	Clinical Features: Seizure (present) , Bilateral tonic-clonic seizure (present) , Periventricular heterotopia (present) , Focal-onset seizure (present) Sex: female

Comment:

This sequence change creates a premature translational stop signal (p.Val2124Glufs*26) in the FLNA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FLNA are known to be pathogenic (PMID: 16684786, 20730588, 26471271). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FLNA-related conditions. 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
47 patients with FLNA associated periventricular nodular heterotopia.	Lange M	Orphanet journal of rare diseases	2015	PMID: 26471271
Combined cardiological and neurological abnormalities due to filamin A gene mutation.	de Wit MC	Clinical research in cardiology : official journal of the German Cardiac Society	2011	PMID: 20730588
Periventricular heterotopia: phenotypic heterogeneity and correlation with Filamin A mutations.	Parrini E	Brain : a journal of neurology	2006	PMID: 16684786

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_001110556.2(FLNA):c.6395_6396del (p.Val2132fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...