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NM_005249.5(FOXG1):c.339del (p.Ala114fs) AND Rett syndrome, congenital variant

Germline classification:
Likely pathogenic (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:
RCV003158017.2

Allele description [Variation Report for NM_005249.5(FOXG1):c.339del (p.Ala114fs)]

NM_005249.5(FOXG1):c.339del (p.Ala114fs)

Gene:
FOXG1:forkhead box G1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
14q12
Genomic location:
Preferred name:
NM_005249.5(FOXG1):c.339del (p.Ala114fs)
HGVS:
  • NC_000014.9:g.28767618del
  • NG_009367.1:g.5538del
  • NM_005249.5:c.339delMANE SELECT
  • NP_005240.3:p.Ala114fs
  • NC_000014.8:g.29236824del
  • NM_005249.5:c.338delCMANE SELECT
Protein change:
A114fs
Molecular consequence:
  • NM_005249.5:c.339del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Rett syndrome, congenital variant
Identifiers:
MONDO: MONDO:0013270; MedGen: C3150705; Orphanet: 3095; OMIM: 613454

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003845982Lifecell International Pvt. Ltd
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Asiangermlineyes1not 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 Lifecell International Pvt. Ltd, SCV003845982.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Asian1not providednot providedclinical testing PubMed (1)

Description

A Heterozygous Frameshift variant c.338delC in Exon 1 of the FOXG1 gene that results in the amino acid substitution p.Ala114fs*78 was identified. The observed variant is novel in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. Based on the above evidence this variant has been classified as Likely Pathogenic according to the ACMG guidelines.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Dec 2, 2023