Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_001083962.2(TCF4):c.1318G>A (p.Gly440Ser)

CA8970233

536801 (ClinVar)

Gene: TCF4
Condition: Pitt-Hopkins syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ea7181ae-d0a7-4ff0-9292-33c4d614b3f2
Approved on: 2025-05-07
Published on: 2025-06-30

HGVS expressions

NM_001083962.2:c.1318G>A
NM_001083962.2(TCF4):c.1318G>A (p.Gly440Ser)
NC_000018.10:g.55254529C>T
CM000680.2:g.55254529C>T
NC_000018.9:g.52921760C>T
CM000680.1:g.52921760C>T
NC_000018.8:g.51072758C>T
NG_011716.1:g.339101G>A
NG_011716.2:g.386465G>A
ENST00000354452.8:c.1318G>A
ENST00000630720.3:c.835G>A
ENST00000635822.2:c.1318G>A
ENST00000635990.2:n.998G>A
ENST00000636400.2:c.1246G>A
ENST00000636751.2:c.*1026G>A
ENST00000636822.2:c.928G>A
ENST00000637115.2:c.*1208G>A
ENST00000637169.2:c.670G>A
ENST00000637239.2:n.1385G>A
ENST00000637250.2:n.1012G>A
ENST00000637923.2:c.916G>A
ENST00000638154.3:c.1345G>A
ENST00000643689.1:c.928G>A
ENST00000674764.1:c.*929G>A
ENST00000675707.1:c.928G>A
ENST00000354452.7:c.1318G>A
ENST00000356073.8:c.1318G>A
ENST00000398339.5:c.1624G>A
ENST00000457482.7:c.838G>A
ENST00000537578.5:c.1246G>A
ENST00000537856.7:c.928G>A
ENST00000540999.5:c.1246G>A
ENST00000543082.5:c.1192G>A
ENST00000544241.6:c.1105G>A
ENST00000561831.7:c.838G>A
ENST00000561992.5:c.928G>A
ENST00000562680.5:n.1409G>A
ENST00000563760.5:n.831G>A
ENST00000564228.5:c.1105G>A
ENST00000564403.6:c.1336G>A
ENST00000564999.5:c.1318G>A
ENST00000565018.6:c.1066G>A
ENST00000566279.5:c.1138G>A
ENST00000566286.5:c.1309G>A
ENST00000567880.5:c.1138G>A
ENST00000568673.5:c.1246G>A
ENST00000568740.5:c.1243G>A
ENST00000570177.6:c.928G>A
ENST00000570287.6:c.838G>A
ENST00000616053.4:c.1066G>A
ENST00000626466.1:n.353G>A
ENST00000626584.2:c.670G>A
ENST00000629387.2:c.1318G>A
ENST00000630720.2:c.835G>A
NM_001083962.1:c.1318G>A
NM_001243226.2:c.1624G>A
NM_001243227.1:c.1246G>A
NM_001243228.1:c.1336G>A
NM_001243230.1:c.1309G>A
NM_001243231.1:c.1192G>A
NM_001243232.1:c.1105G>A
NM_001243233.1:c.928G>A
NM_001243234.1:c.838G>A
NM_001243235.1:c.838G>A
NM_001243236.1:c.838G>A
NM_001306207.1:c.1246G>A
NM_001306208.1:c.1105G>A
NM_003199.2:c.1318G>A
NM_001330604.2:c.1315G>A
NM_001330605.2:c.928G>A
NM_001348211.1:c.1192G>A
NM_001348212.1:c.928G>A
NM_001348213.1:c.928G>A
NM_001348214.1:c.835G>A
NM_001348215.1:c.670G>A
NM_001348216.1:c.838G>A
NM_001348217.1:c.1246G>A
NM_001348218.1:c.1246G>A
NM_001348219.1:c.1246G>A
NM_001348220.1:c.1243G>A
NM_001243226.3:c.1624G>A
NM_001243227.2:c.1246G>A
NM_001243228.2:c.1336G>A
NM_001243231.2:c.1192G>A
NM_001243233.2:c.928G>A
NM_001243234.2:c.838G>A
NM_001243235.2:c.838G>A
NM_001243236.2:c.838G>A
NM_001330604.3:c.1315G>A
NM_001330605.3:c.928G>A
NM_001348211.2:c.1192G>A
NM_001348212.2:c.928G>A
NM_001348213.2:c.928G>A
NM_001348214.2:c.835G>A
NM_001348215.2:c.670G>A
NM_001348216.2:c.838G>A
NM_001348218.2:c.1246G>A
NM_001348219.2:c.1246G>A
NM_001369567.1:c.1318G>A
NM_001369568.1:c.1318G>A
NM_001369569.1:c.1315G>A
NM_001369570.1:c.1315G>A
NM_001369571.1:c.1318G>A
NM_001369572.1:c.1318G>A
NM_001369573.1:c.1315G>A
NM_001369574.1:c.1315G>A
NM_001369575.1:c.1246G>A
NM_001369576.1:c.1243G>A
NM_001369577.1:c.1243G>A
NM_001369578.1:c.1243G>A
NM_001369579.1:c.1243G>A
NM_001369580.1:c.1243G>A
NM_001369581.1:c.1243G>A
NM_001369582.1:c.1246G>A
NM_001369583.1:c.1246G>A
NM_001369584.1:c.1243G>A
NM_001369585.1:c.1243G>A
NM_001369586.1:c.1249G>A
NM_003199.3:c.1318G>A
NM_001243230.2:c.1309G>A
More

Benign

Met criteria codes 1
BA1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TCF4 Version 4.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The highest population minor allele frequency of the p.Gly440Ser variant in TCF4 in gnomAD v4.1 is 0.0004063 in the South Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1). In the absence of conflicting evidence, this is sufficient evidence to classify as benign based on the specifications defined by the ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel (TCF4 Specifications v.4.0; curation approved on [5/7/2025]).
Met criteria codes
BA1
The highest population minor allele frequency of the p.Gly440Ser variant in TCF4 in gnomAD v4.1 is 0.0004063 in the South Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1).
Curation History
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