NM_001904.4(CTNNB1):c.696del (p.Phe232fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 11, 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:: RCV002002572.4

Allele description [Variation Report for NM_001904.4(CTNNB1):c.696del (p.Phe232fs)]

NM_001904.4(CTNNB1):c.696del (p.Phe232fs)

Genes:

LOC126806658:BRD4-independent group 4 enhancer GRCh37_chr3:41265899-41267098 [Gene]
CTNNB1:catenin beta 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p22.1

Genomic location:

Preferred name:

NM_001904.4(CTNNB1):c.696del (p.Phe232fs)

HGVS:

NC_000003.12:g.41225534del
NG_013302.2:g.31084del
NM_001098209.2:c.696del
NM_001098210.2:c.696del
NM_001330729.2:c.675del
NM_001904.4:c.696delMANE SELECT
NP_001091679.1:p.Phe232fs
NP_001091680.1:p.Phe232fs
NP_001317658.1:p.Phe225fs
NP_001895.1:p.Phe232fs
LRG_1108t1:c.696del
LRG_1108:g.31084del
LRG_1108p1:p.Phe232fs
NC_000003.11:g.41267023del
NC_000003.11:g.41267025del

Protein change:

F225fs

Links:

dbSNP: rs2125623360

NCBI 1000 Genomes Browser:

rs2125623360

Molecular consequence:

NM_001098209.2:c.696del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001098210.2:c.696del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330729.2:c.675del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001904.4:c.696del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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gi|38407630|gnl|dbEST|20452023|emb| 889.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002231969	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 11, 2021)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 23033978, 24614104, 25326669, 26350204, 28575650, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002231969

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 11, 2021)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

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

Citations

PubMed

Diagnostic exome sequencing in persons with severe intellectual disability.

de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen C, del Rosario M, Hoischen A, Scheffer H, de Vries BB, Brunner HG, Veltman JA, Vissers LE.

N Engl J Med. 2012 Nov 15;367(20):1921-9. doi: 10.1056/NEJMoa1206524. Epub 2012 Oct 3.

PubMed [citation]

PMID:: 23033978

Dominant β-catenin mutations cause intellectual disability with recognizable syndromic features.

Tucci V, Kleefstra T, Hardy A, Heise I, Maggi S, Willemsen MH, Hilton H, Esapa C, Simon M, Buenavista MT, McGuffin LJ, Vizor L, Dodero L, Tsaftaris S, Romero R, Nillesen WN, Vissers LE, Kempers MJ, Vulto-van Silfhout AT, Iqbal Z, Orlando M, Maccione A, et al.

J Clin Invest. 2014 Apr;124(4):1468-82. doi: 10.1172/JCI70372. Epub 2014 Mar 10.

PubMed [citation]

PMID:: 24614104
PMCID:: PMC3973091

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002231969.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with CTNNB1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Phe232Leufs*10) in the CTNNB1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CTNNB1 are known to be pathogenic (PMID: 23033978, 24614104, 25326669, 26350204, 28575650).

#	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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