NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 19, 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:: RCV001951257.4

Allele description [Variation Report for NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter)]

NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter)

Gene:

CTNNB1:catenin beta 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.1

Genomic location:

Preferred name:

NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter)

HGVS:

NC_000003.12:g.41225733A>T
NG_013302.2:g.31283A>T
NM_001098209.2:c.808A>T
NM_001098210.2:c.808A>T
NM_001330729.2:c.787A>T
NM_001904.4:c.808A>TMANE SELECT
NP_001091679.1:p.Lys270Ter
NP_001091680.1:p.Lys270Ter
NP_001317658.1:p.Lys263Ter
NP_001895.1:p.Lys270Ter
LRG_1108t1:c.808A>T
LRG_1108:g.31283A>T
LRG_1108p1:p.Lys270Ter
NC_000003.11:g.41267224A>T

Protein change:

K263*

Links:

dbSNP: rs2125624259

NCBI 1000 Genomes Browser:

rs2125624259

Molecular consequence:

NM_001098209.2:c.808A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001098210.2:c.808A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001330729.2:c.787A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001904.4:c.808A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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KIRREL1 [Ursus maritimus]
KIRREL1 [Ursus maritimus]
Gene ID:103672143

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002243128	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 19, 2022)	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

SCV002243128

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 19, 2022)

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, SCV002243128.3

#	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. ClinVar contains an entry for this variant (Variation ID: 1456658). This variant has not been reported in the literature in individuals affected with CTNNB1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys270*) 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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