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 computer assertion could be determined for this classification!

Variant: NM_001083962.2(TCF4):c.466C>A (p.Pro156Thr)

CA8970510

664780 (ClinVar)

Gene: TCF4 (HGNC:6925)
Condition: Pitt-Hopkins syndrome (MONDO:0012589)
Inheritance Mode: Autosomal dominant inheritance
UUID: 009efeaf-274d-43f3-83d3-095679e3c249
Approved on: 2024-06-25
Published on: 2024-08-23

HGVS expressions

NM_001083962.2:c.466C>A
NM_001083962.2(TCF4):c.466C>A (p.Pro156Thr)
NC_000018.10:g.55350907G>T
CM000680.2:g.55350907G>T
NC_000018.9:g.53018138G>T
CM000680.1:g.53018138G>T
NC_000018.8:g.51169136G>T
NG_011716.1:g.242723C>A
NG_011716.2:g.290087C>A
ENST00000354452.8:c.466C>A
ENST00000635822.2:c.466C>A
ENST00000635990.2:n.146C>A
ENST00000636400.2:c.394C>A
ENST00000636751.2:c.*174C>A
ENST00000636822.2:c.76C>A
ENST00000637115.2:c.*356C>A
ENST00000637239.2:n.533C>A
ENST00000637250.2:n.160C>A
ENST00000638154.3:c.496C>A
ENST00000643689.1:c.76C>A
ENST00000674764.1:c.*77C>A
ENST00000675707.1:c.76C>A
ENST00000354452.7:c.466C>A
ENST00000356073.8:c.466C>A
ENST00000398339.5:c.772C>A
ENST00000537578.5:c.394C>A
ENST00000537856.7:c.76C>A
ENST00000540999.5:c.394C>A
ENST00000543082.5:c.340C>A
ENST00000544241.6:c.253C>A
ENST00000561992.5:c.76C>A
ENST00000562030.3:c.76C>A
ENST00000562607.5:c.76C>A
ENST00000562638.5:c.76C>A
ENST00000562680.5:n.557C>A
ENST00000563686.5:n.321C>A
ENST00000563824.5:c.394C>A
ENST00000563888.6:c.391C>A
ENST00000564228.5:c.253C>A
ENST00000564343.5:c.394C>A
ENST00000564403.6:c.466C>A
ENST00000564999.5:c.466C>A
ENST00000565018.6:c.297+52547C>A
ENST00000565580.3:n.298+52547C>A
ENST00000565908.6:c.394C>A
ENST00000566279.5:c.369+52547C>A
ENST00000566286.5:c.460C>A
ENST00000566376.3:n.146C>A
ENST00000566514.5:c.427C>A
ENST00000566777.5:c.76C>A
ENST00000567880.5:c.369+52547C>A
ENST00000568147.5:c.430C>A
ENST00000568169.5:c.478C>A
ENST00000568186.5:c.76C>A
ENST00000568673.5:c.394C>A
ENST00000568740.5:c.391C>A
ENST00000569012.5:c.76C>A
ENST00000570177.6:c.76C>A
ENST00000590810.5:c.112C>A
ENST00000616053.4:c.297+52547C>A
ENST00000625849.2:n.326C>A
ENST00000625925.2:c.76C>A
ENST00000626425.2:c.391C>A
ENST00000626584.2:c.-100+52547C>A
ENST00000626595.2:c.466C>A
ENST00000627136.2:n.440C>A
ENST00000627685.2:c.394C>A
ENST00000627784.2:c.463C>A
ENST00000628078.2:c.76C>A
ENST00000628636.2:c.76C>A
ENST00000629343.2:c.76C>A
ENST00000629387.2:c.466C>A
ENST00000630268.2:c.76C>A
ENST00000630319.2:c.235C>A
ENST00000630712.2:c.76C>A
ENST00000630828.2:c.256C>A
ENST00000631043.2:n.265C>A
NM_001083962.1:c.466C>A
NM_001243226.2:c.772C>A
NM_001243227.1:c.394C>A
NM_001243228.1:c.466C>A
NM_001243230.1:c.460C>A
NM_001243231.1:c.340C>A
NM_001243232.1:c.253C>A
NM_001243233.1:c.76C>A
NM_001306207.1:c.394C>A
NM_001306208.1:c.253C>A
NM_003199.2:c.466C>A
NM_001330604.2:c.466C>A
NM_001330605.2:c.76C>A
NM_001348211.1:c.340C>A
NM_001348212.1:c.76C>A
NM_001348213.1:c.76C>A
NM_001348217.1:c.394C>A
NM_001348218.1:c.394C>A
NM_001348219.1:c.394C>A
NM_001348220.1:c.391C>A
NM_001243226.3:c.772C>A
NM_001243227.2:c.394C>A
NM_001243228.2:c.466C>A
NM_001243231.2:c.340C>A
NM_001243233.2:c.76C>A
NM_001330604.3:c.466C>A
NM_001330605.3:c.76C>A
NM_001348211.2:c.340C>A
NM_001348212.2:c.76C>A
NM_001348213.2:c.76C>A
NM_001348218.2:c.394C>A
NM_001348219.2:c.394C>A
NM_001369567.1:c.466C>A
NM_001369568.1:c.466C>A
NM_001369569.1:c.463C>A
NM_001369570.1:c.463C>A
NM_001369571.1:c.466C>A
NM_001369572.1:c.466C>A
NM_001369573.1:c.463C>A
NM_001369574.1:c.466C>A
NM_001369575.1:c.394C>A
NM_001369576.1:c.391C>A
NM_001369577.1:c.394C>A
NM_001369578.1:c.391C>A
NM_001369579.1:c.394C>A
NM_001369580.1:c.394C>A
NM_001369581.1:c.391C>A
NM_001369582.1:c.394C>A
NM_001369583.1:c.394C>A
NM_001369584.1:c.391C>A
NM_001369585.1:c.391C>A
NM_001369586.1:c.394C>A
NM_003199.3:c.466C>A
NM_001243230.2:c.460C>A
More

Likely Benign

Met criteria codes 2
BS2 BP4
Not Met criteria codes 1
BS1

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 3.0.0

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.Pro156Thr variant in TCF4 in gnomAD v4.1 is 0.000067 in the Admixed American population (not sufficient to meet BS1 criteria). The p.Pro156Thr variant is observed in at least 2 unaffected individuals (Internal database - Ambry) (BS2). Computational analysis prediction tools suggest that the p.Pro156Thr variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). In summary, the p.Pro156Thr variant in TCF4 is classified as likely benign based on the ACMG/AMP criteria (BS2, BP4).
Met criteria codes
BS2
The p.Pro156Thr variant is observed in at least 2 unaffected individuals (Internal database - Ambry) (BS2).
BP4
Computational analysis prediction tools suggest that the p.Pro156Thr variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4).
Not Met criteria codes
BS1
The highest population minor allele frequency of the p.Pro156Thr variant in TCF4 in gnomAD v4.1 is 0.000067 in the Admixed American population (not sufficient to meet BS1 criteria).
Curation History
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