NM_001903.5(CTNNA1):c.362G>A (p.Arg121Gln) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Mar 1, 2024
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:: RCV001020757.3

Allele description [Variation Report for NM_001903.5(CTNNA1):c.362G>A (p.Arg121Gln)]

NM_001903.5(CTNNA1):c.362G>A (p.Arg121Gln)

Gene:

CTNNA1:catenin alpha 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q31.2

Genomic location:

Preferred name:

NM_001903.5(CTNNA1):c.362G>A (p.Arg121Gln)

HGVS:

NC_000005.10:g.138810098G>A
NG_047029.1:g.61703G>A
NM_001290307.3:c.362G>A
NM_001290309.3:c.53G>A
NM_001290310.3:c.-5-3G>A
NM_001323982.2:c.362G>A
NM_001323983.1:c.362G>A
NM_001323984.2:c.362G>A
NM_001323985.2:c.362G>A
NM_001323986.2:c.362G>A
NM_001903.5:c.362G>AMANE SELECT
NP_001277236.1:p.Arg121Gln
NP_001277238.1:p.Arg18Gln
NP_001310911.1:p.Arg121Gln
NP_001310912.1:p.Arg121Gln
NP_001310913.1:p.Arg121Gln
NP_001310914.1:p.Arg121Gln
NP_001310915.1:p.Arg121Gln
NP_001894.2:p.Arg121Gln
NC_000005.9:g.138145787G>A
NM_001903.2:c.362G>A
NM_001903.3:c.362G>A

Protein change:

R121Q

Links:

dbSNP: rs749878552

NCBI 1000 Genomes Browser:

rs749878552

Molecular consequence:

NM_001290310.3:c.-5-3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001290307.3:c.362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001290309.3:c.53G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323982.2:c.362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323983.1:c.362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323984.2:c.362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323985.2:c.362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323986.2:c.362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001903.5:c.362G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001182274	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Mar 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001182274

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Mar 1, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Loss-of-function variants in CTNNA1 detected on multigene panel testing in individuals with gastric or breast cancer.

Clark DF, Michalski ST, Tondon R, Nehoray B, Ebrahimzadeh J, Hughes SK, Soper ER, Domchek SM, Rustgi AK, Pineda-Alvarez D, Anderson MJ, Katona BW.

Genet Med. 2020 May;22(5):840-846. doi: 10.1038/s41436-020-0753-1. Epub 2020 Feb 13.

PubMed [citation]

PMID:: 32051609
PMCID:: PMC7200596

Details of each submission

From Ambry Genetics, SCV001182274.4

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: May 1, 2024

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