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NM_005249.5(FOXG1):c.634del (p.Ile211_Met212insTer) AND Rett syndrome, congenital variant

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 28, 2021
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:
RCV001781127.5

Allele description [Variation Report for NM_005249.5(FOXG1):c.634del (p.Ile211_Met212insTer)]

NM_005249.5(FOXG1):c.634del (p.Ile211_Met212insTer)

Gene:
FOXG1:forkhead box G1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
14q12
Genomic location:
Preferred name:
NM_005249.5(FOXG1):c.634del (p.Ile211_Met212insTer)
HGVS:
  • NC_000014.9:g.28767913del
  • NG_009367.1:g.5833del
  • NM_005249.5:c.634delMANE SELECT
  • NP_005240.3:p.Ile211_Met212insTer
  • NC_000014.8:g.29237119del
  • NM_005249.5:c.634delAMANE SELECT
Links:
dbSNP: rs2138661266
NCBI 1000 Genomes Browser:
rs2138661266
Molecular consequence:
  • NM_005249.5:c.634del - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Rett syndrome, congenital variant
Identifiers:
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
SCV002043772Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 28, 2021) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes11not 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 Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV002043772.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.634delA variant is not present in publicly available population databases like 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC) Genome Aggregation Database (gnomAD) and dbSNP. The variant is not present in Indian Exome Database and in our in-house exome database. The variant was not earlier reported to ClinVar, Human Genome Mutation Database (HGMD) and OMIM databases in any affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome etc. predicted this variant to be likely disease causing. The deletion causes a frameshift and creates a premature stop codon at the 212 amino acid position of the altered transcript that either may result into a truncated protein or nonsense mediated decay of the mRNA.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot provideddiscovery1not provided1not provided

Last Updated: Feb 16, 2025