U.S. flag

An official website of the United States government

NM_001349338.3(FOXP1):c.116G>C (p.Gly39Ala) AND Intellectual disability-severe speech delay-mild dysmorphism syndrome

Germline classification:
Uncertain significance (1 submission)
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:
RCV002510725.3

Allele description [Variation Report for NM_001349338.3(FOXP1):c.116G>C (p.Gly39Ala)]

NM_001349338.3(FOXP1):c.116G>C (p.Gly39Ala)

Gene:
FOXP1:forkhead box P1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p13
Genomic location:
Preferred name:
NM_001349338.3(FOXP1):c.116G>C (p.Gly39Ala)
HGVS:
  • NC_000003.12:g.71198266C>G
  • NG_028243.1:g.390724G>C
  • NM_001012505.2:c.116G>C
  • NM_001244808.3:c.116G>C
  • NM_001244810.2:c.116G>C
  • NM_001244812.3:c.116G>C
  • NM_001244814.3:c.116G>C
  • NM_001244816.2:c.116G>C
  • NM_001349338.3:c.116G>CMANE SELECT
  • NM_001349339.1:c.116G>C
  • NM_001349340.3:c.116G>C
  • NM_001349341.3:c.116G>C
  • NM_032682.6:c.116G>C
  • NP_001012523.1:p.Gly39Ala
  • NP_001231737.1:p.Gly39Ala
  • NP_001231739.1:p.Gly39Ala
  • NP_001231741.1:p.Gly39Ala
  • NP_001231743.1:p.Gly39Ala
  • NP_001231745.1:p.Gly39Ala
  • NP_001336267.1:p.Gly39Ala
  • NP_001336268.1:p.Gly39Ala
  • NP_001336269.1:p.Gly39Ala
  • NP_001336270.1:p.Gly39Ala
  • NP_116071.2:p.Gly39Ala
  • NC_000003.11:g.71247417C>G
  • NM_032682.5:c.116G>C
  • NR_146142.3:n.720G>C
  • NR_146143.3:n.720G>C
Protein change:
G39A
Molecular consequence:
  • NM_001012505.2:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001244808.3:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001244810.2:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001244812.3:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001244814.3:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001244816.2:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349338.3:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349339.1:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349340.3:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349341.3:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032682.6:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146142.3:n.720G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146143.3:n.720G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Intellectual disability-severe speech delay-mild dysmorphism syndrome (IDDLA)
Synonyms:
Mental retardation with language impairment and autistic features; Intellectual developmental disorder with language impairment AND with or without autistic features
Identifiers:
MONDO: MONDO:0013352; MedGen: C4013764; Orphanet: 391372; OMIM: 613670

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002820268Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot 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 Neuberg Centre For Genomic Medicine, NCGM, SCV002820268.1

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

Description

The missense variant p.G39A in FOXP1 (NM_032682.5) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.G39A variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. There is a small physicochemical difference between glycine and alanine, which is not likely to impact secondary protein structure as these residues share similar properties. The p.G39A missense variant is predicted to be damaging by both SIFT and PolyPhen2. The glycine residue at codon 39 of FOXP1 is conserved in all mammalian species. The nucleotide c.116 in FOXP1 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance

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

Last Updated: Dec 7, 2024