NM_001083962.2(TCF4):c.1147-3C>G AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 6, 2020
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:: RCV001174968.1

Allele description [Variation Report for NM_001083962.2(TCF4):c.1147-3C>G]

NM_001083962.2(TCF4):c.1147-3C>G

Gene:

TCF4:transcription factor 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.2

Genomic location:

Preferred name:

NM_001083962.2(TCF4):c.1147-3C>G

HGVS:

NC_000018.10:g.55254703G>C
NG_011716.2:g.386291C>G
NM_001083962.2:c.1147-3C>GMANE SELECT
NM_001243226.3:c.1453-3C>G
NM_001243227.2:c.1075-3C>G
NM_001243228.2:c.1165-3C>G
NM_001243230.2:c.1138-3C>G
NM_001243231.2:c.1021-3C>G
NM_001243232.1:c.934-3C>G
NM_001243233.2:c.757-3C>G
NM_001243234.2:c.667-3C>G
NM_001243235.2:c.667-3C>G
NM_001243236.2:c.667-3C>G
NM_001306207.1:c.1075-3C>G
NM_001306208.1:c.934-3C>G
NM_001330604.3:c.1144-3C>G
NM_001330605.3:c.757-3C>G
NM_001348211.2:c.1021-3C>G
NM_001348212.2:c.757-3C>G
NM_001348213.2:c.757-3C>G
NM_001348214.2:c.664-3C>G
NM_001348215.2:c.499-3C>G
NM_001348216.2:c.667-3C>G
NM_001348217.1:c.1075-3C>G
NM_001348218.2:c.1075-3C>G
NM_001348219.2:c.1075-3C>G
NM_001348220.1:c.1072-3C>G
NM_001369567.1:c.1147-3C>G
NM_001369568.1:c.1147-3C>G
NM_001369569.1:c.1144-3C>G
NM_001369570.1:c.1144-3C>G
NM_001369571.1:c.1147-3C>G
NM_001369572.1:c.1147-3C>G
NM_001369573.1:c.1144-3C>G
NM_001369574.1:c.1144-3C>G
NM_001369575.1:c.1075-3C>G
NM_001369576.1:c.1072-3C>G
NM_001369577.1:c.1072-3C>G
NM_001369578.1:c.1072-3C>G
NM_001369579.1:c.1072-3C>G
NM_001369580.1:c.1072-3C>G
NM_001369581.1:c.1072-3C>G
NM_001369582.1:c.1075-3C>G
NM_001369583.1:c.1075-3C>G
NM_001369584.1:c.1072-3C>G
NM_001369585.1:c.1072-3C>G
NM_001369586.1:c.1078-3C>G
NM_003199.3:c.1147-3C>G
NC_000018.9:g.52921934G>C
NM_001083962.1:c.1147-3C>G

Links:

dbSNP: rs2056333687

NCBI 1000 Genomes Browser:

rs2056333687

Molecular consequence:

NM_001083962.2:c.1147-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243226.3:c.1453-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243227.2:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243228.2:c.1165-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243230.2:c.1138-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243231.2:c.1021-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243232.1:c.934-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243233.2:c.757-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243234.2:c.667-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243235.2:c.667-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001243236.2:c.667-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001306207.1:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001306208.1:c.934-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330604.3:c.1144-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330605.3:c.757-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348211.2:c.1021-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348212.2:c.757-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348213.2:c.757-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348214.2:c.664-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348215.2:c.499-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348216.2:c.667-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348217.1:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348218.2:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348219.2:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001348220.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369567.1:c.1147-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369568.1:c.1147-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369569.1:c.1144-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369570.1:c.1144-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369571.1:c.1147-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369572.1:c.1147-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369573.1:c.1144-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369574.1:c.1144-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369575.1:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369576.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369577.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369578.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369579.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369580.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369581.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369582.1:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369583.1:c.1075-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369584.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369585.1:c.1072-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001369586.1:c.1078-3C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_003199.3:c.1147-3C>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Homo sapiens dishevelled associated activator of morphogenesis 2 (DAAM2), transc...
Homo sapiens dishevelled associated activator of morphogenesis 2 (DAAM2), transcript variant 2, mRNA
gi|1890254529|ref|NM_015345.4|

Nucleotide
ribosomal protein S12, partial (chloroplast) [Scheuchzeria palustris]
ribosomal protein S12, partial (chloroplast) [Scheuchzeria palustris]
gi|37721174|gb|AAN31963.1|

Protein
histone H1.10 [Gallus gallus]
histone H1.10 [Gallus gallus]
gi|475504775|ref|NP_001264297.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001338450	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Apr 6, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001338450

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Apr 6, 2020)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001338450.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: TCF4 c.1147-3C>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: three predict the variant abolishes a 3' acceptor site, and two predict the variant creates a 3' acceptor site 2 nucleotides upstream from the original, canonical splice site; that would result in a frameshift at the protein level. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 226208 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1147-3C>G in individuals affected with Pitt-Hopkins syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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