VCV002098207.4 - ClinVar

NM_001349338.3(FOXP1):c.1556T>C (p.Leu519Pro)

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.

Conflicting classifications of pathogenicity
Pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001349338.3(FOXP1):c.1556T>C (p.Leu519Pro)

Variation ID: 2098207 Accession: VCV002098207.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 3p13 3: 70972651 (GRCh38) [ NCBI UCSC ] 3: 71021802 (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 8, 2023	Feb 20, 2024	Aug 10, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001349338.3:c.1556T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001336267.1:p.Leu519Pro	missense
NM_001244808.3:c.1553T>C	NP_001231737.1:p.Leu518Pro	missense
NM_001244810.2:c.1531-471T>C		intron variant
NM_001244812.3:c.1328T>C	NP_001231741.1:p.Leu443Pro	missense
NM_001244813.3:c.1256T>C	NP_001231742.1:p.Leu419Pro	missense
NM_001244814.3:c.1556T>C	NP_001231743.1:p.Leu519Pro	missense
NM_001244815.2:c.1256T>C	NP_001231744.2:p.Leu419Pro	missense
NM_001244816.2:c.1556T>C	NP_001231745.1:p.Leu519Pro	missense
NM_001349337.2:c.1253T>C	NP_001336266.2:p.Leu418Pro	missense
NM_001349339.1:c.1556T>C	NP_001336268.1:p.Leu519Pro	missense
NM_001349340.3:c.1556T>C	NP_001336269.1:p.Leu519Pro	missense
NM_001349341.3:c.1553T>C	NP_001336270.1:p.Leu518Pro	missense
NM_001349342.3:c.1256T>C	NP_001336271.1:p.Leu419Pro	missense
NM_001349343.3:c.1253T>C	NP_001336272.1:p.Leu418Pro	missense
NM_001349344.3:c.1253T>C	NP_001336273.1:p.Leu418Pro	missense
NM_001370548.1:c.1253T>C	NP_001357477.1:p.Leu418Pro	missense
NM_032682.5:c.1556T>C
NM_032682.6:c.1556T>C	NP_116071.2:p.Leu519Pro	missense
NR_146142.3:n.2072T>C		non-coding transcript variant
NR_146143.3:n.2069T>C		non-coding transcript variant
NC_000003.12:g.70972651A>G
NC_000003.11:g.71021802A>G
NG_028243.1:g.616339T>C

... more HGVS ... less HGVS

Protein change

L419P, L518P, L519P, L418P, L443P

Other names

Canonical SPDI

NC_000003.12:70972650:A:G

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.
FOXP1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	840	919

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.
not provided	Pathogenic (1)	criteria provided, single submitter	Aug 10, 2022	RCV003019137.4
Intellectual disability-severe speech delay-mild dysmorphism syndrome	Uncertain significance (1)	criteria provided, single submitter	Aug 1, 2019	RCV003146730.4

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.
Uncertain significance (Aug 01, 2019)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Intellectual disability-severe speech delay-mild dysmorphism syndrome Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV003833655.2 First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024
Pathogenic (Aug 10, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003310647.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Publications: PubMed (1) PubMed: 33427368 Comment: Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) … (more) Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt FOXP1 protein function. This missense change has been observed in individual(s) with intellectual disability syndrome (PMID: 33427368). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 519 of the FOXP1 protein (p.Leu519Pro). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt FOXP1 protein function. This missense change has been observed in individual(s) with intellectual disability syndrome (PMID: 33427368). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 519 of the FOXP1 protein (p.Leu519Pro). 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
Novel FOXP1 pathogenic variants in two Indian subjects with syndromic intellectual disability.	Moirangthem A	American journal of medical genetics. Part A	2021	PMID: 33427368

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_001349338.3(FOXP1):c.1556T>C (p.Leu519Pro)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...