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NM_001378418.1(TCF20):c.4187G>A (p.Gly1396Glu) AND Developmental delay with variable intellectual impairment and behavioral abnormalities

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 9, 2022
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:
RCV002286551.1

Allele description [Variation Report for NM_001378418.1(TCF20):c.4187G>A (p.Gly1396Glu)]

NM_001378418.1(TCF20):c.4187G>A (p.Gly1396Glu)

Gene:
TCF20:transcription factor 20 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.2
Genomic location:
Preferred name:
NM_001378418.1(TCF20):c.4187G>A (p.Gly1396Glu)
Other names:
p.Gly1396Glu
HGVS:
  • NC_000022.11:g.42211119C>T
  • NG_028982.3:g.137498G>A
  • NM_001378418.1:c.4187G>AMANE SELECT
  • NM_005650.4:c.4187G>A
  • NM_181492.3:c.4187G>A
  • NP_001365347.1:p.Gly1396Glu
  • NP_005641.1:p.Gly1396Glu
  • NP_852469.1:p.Gly1396Glu
  • LRG_1025t1:c.4187G>A
  • LRG_1025t2:c.4187G>A
  • LRG_1025:g.137498G>A
  • LRG_1025p1:p.Gly1396Glu
  • LRG_1025p2:p.Gly1396Glu
  • NC_000022.10:g.42607125C>T
Protein change:
G1396E
Links:
dbSNP: rs774041838
NCBI 1000 Genomes Browser:
rs774041838
Molecular consequence:
  • NM_001378418.1:c.4187G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005650.4:c.4187G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181492.3:c.4187G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
Unknown function
Observations:
1

Condition(s)

Name:
Developmental delay with variable intellectual impairment and behavioral abnormalities
Identifiers:
MONDO: MONDO:0032745; MedGen: C5193092; OMIM: 618430

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002574766Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 9, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Hindugermlineyes1not 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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV002574766.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Hindu1not providednot providedclinical testing PubMed (1)

Description

A heterozygous missense variation in exon 2 of the TCF20 gene that results in the amino acid substitution of Glutamic acid for Glycine at codon 1396 was detected. The observed variant c.4187G>A (p.Gly1396Glu) has not been reported in the 1000 genomes and has a minor allele frequency of 0.0006% in the gnomAD database. The in silico prediction of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by LRT and SIFT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a variant of uncertain significance.

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

Last Updated: Oct 8, 2022