ClinVar Genomic variation as it relates to human health
NM_001349338.3(FOXP1):c.1507C>T (p.Arg503Ter)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001349338.3(FOXP1):c.1507C>T (p.Arg503Ter)
Variation ID: 211038 Accession: VCV000211038.17
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 3p13 3: 70976964 (GRCh38) [ NCBI UCSC ] 3: 71026115 (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 5, 2015 Feb 14, 2024 Sep 14, 2022 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_001349338.3:c.1507C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001336267.1:p.Arg503Ter nonsense NM_001244808.3:c.1504C>T NP_001231737.1:p.Arg502Ter nonsense NM_001244810.2:c.1507C>T NP_001231739.1:p.Arg503Ter nonsense NM_001244812.3:c.1279C>T NP_001231741.1:p.Arg427Ter nonsense NM_001244813.3:c.1207C>T NP_001231742.1:p.Arg403Ter nonsense NM_001244814.3:c.1507C>T NP_001231743.1:p.Arg503Ter nonsense NM_001244815.2:c.1207C>T NP_001231744.2:p.Arg403Ter nonsense NM_001244816.2:c.1507C>T NP_001231745.1:p.Arg503Ter nonsense NM_001349337.2:c.1204C>T NP_001336266.2:p.Arg402Ter nonsense NM_001349340.3:c.1507C>T NP_001336269.1:p.Arg503Ter nonsense NM_001349341.3:c.1504C>T NP_001336270.1:p.Arg502Ter nonsense NM_001349342.3:c.1207C>T NP_001336271.1:p.Arg403Ter nonsense NM_001349343.3:c.1204C>T NP_001336272.1:p.Arg402Ter nonsense NM_001349344.3:c.1204C>T NP_001336273.1:p.Arg402Ter nonsense NM_001370548.1:c.1204C>T NP_001357477.1:p.Arg402Ter nonsense NM_032682.6:c.1507C>T NP_116071.2:p.Arg503Ter nonsense NR_146142.3:n.2023C>T non-coding transcript variant NR_146143.3:n.2020C>T non-coding transcript variant NC_000003.12:g.70976964G>A NC_000003.11:g.71026115G>A NG_028243.1:g.612026C>T - Protein change
- R503*, R402*, R502*, R427*, R403*
- Other names
- -
- Canonical SPDI
- NC_000003.12:70976963:G:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
Global minor allele
frequency (GMAF) HelpThe 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.
-
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 | ||
---|---|---|---|---|---|---|
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 |
804 | 880 | |
LOC126806714 | - | - | - | GRCh38 | - | 60 |
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. |
---|---|---|---|---|
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Feb 20, 2020 | RCV000195136.9 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Sep 14, 2022 | RCV000423150.10 |
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
(Oct 14, 2014)
|
criteria provided, single submitter
Method: clinical testing
|
Mental retardation with language impairment and autistic features
Affected status: yes
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV000247423.1
First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015 |
|
|
Pathogenic
(Feb 20, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
Intellectual disability-severe speech delay-mild dysmorphism syndrome
Affected status: yes
Allele origin:
unknown
|
Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001368481.2
First in ClinVar: Jul 04, 2020 Last updated: Dec 12, 2020 |
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS4_MOD,PM2.
|
|
Pathogenic
(Sep 14, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000535158.7
First in ClinVar: Mar 08, 2017 Last updated: Mar 04, 2023 |
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28191890, 27824329, 31981491, 28714951, 34588003, 31332282, 25363768) (less)
|
|
Pathogenic
(Jul 30, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV001389301.4
First in ClinVar: Jul 16, 2020 Last updated: Feb 14, 2024 |
Comment:
This variant is also known as p.Arg505*. This premature translational stop signal has been observed in individual(s) with FOXP1-related disease (PMID: 25363768, 27824329; Invitae). In … (more)
This variant is also known as p.Arg505*. This premature translational stop signal has been observed in individual(s) with FOXP1-related disease (PMID: 25363768, 27824329; Invitae). 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 creates a premature translational stop signal (p.Arg503*) in the FOXP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FOXP1 are known to be pathogenic (PMID: 28735298). ClinVar contains an entry for this variant (Variation ID: 211038). For these reasons, this variant has been classified as Pathogenic. (less)
|
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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
FOXP1-related intellectual disability syndrome: a recognisable entity. | Meerschaut I | Journal of medical genetics | 2017 | PMID: 28735298 |
De novo genic mutations among a Chinese autism spectrum disorder cohort. | Wang T | Nature communications | 2016 | PMID: 27824329 |
The contribution of de novo coding mutations to autism spectrum disorder. | Iossifov I | Nature | 2014 | PMID: 25363768 |
Text-mined citations for rs797045584 ...
HelpRecord last updated Feb 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.