NM_000051.4(ATM):c.7397C>T (p.Ala2466Val) AND Ataxia-telangiectasia syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 1, 2023
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:: RCV003500742.2

Allele description [Variation Report for NM_000051.4(ATM):c.7397C>T (p.Ala2466Val)]

NM_000051.4(ATM):c.7397C>T (p.Ala2466Val)

Genes:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.7397C>T (p.Ala2466Val)

HGVS:

NC_000011.10:g.108330303C>T
NG_009830.1:g.112472C>T
NG_054724.1:g.144530G>A
NM_000051.4:c.7397C>TMANE SELECT
NM_001330368.2:c.641-21232G>A
NM_001351110.2:c.*38+4917G>A
NM_001351834.2:c.7397C>T
NP_000042.3:p.Ala2466Val
NP_000042.3:p.Ala2466Val
NP_001338763.1:p.Ala2466Val
LRG_135t1:c.7397C>T
LRG_135:g.112472C>T
LRG_135p1:p.Ala2466Val
NC_000011.9:g.108201030C>T
NM_000051.3:c.7397C>T

Protein change:

A2466V

Molecular consequence:

NM_001330368.2:c.641-21232G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+4917G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.7397C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.7397C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Ataxia-telangiectasia syndrome (AT)
Synonyms:: Louis-Bar syndrome; Cerebello-oculocutaneous telangiectasia; Immunodeficiency with ataxia telangiectasia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008840; MedGen: C0004135; Orphanet: 100; OMIM: 208900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004296158	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11746755, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004296158

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2023)

germline

clinical testing

PubMed (2)
[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

Screening breast cancer patients for ATM mutations and polymorphisms by using denaturing high-performance liquid chromatography.

Atencio DP, Iannuzzi CM, Green S, Stock RG, Bernstein JL, Rosenstein BS.

Environ Mol Mutagen. 2001;38(2-3):200-8.

PubMed [citation]

PMID:: 11746755

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004296158.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2466 of the ATM protein (p.Ala2466Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer (PMID: 11746755). ClinVar contains an entry for this variant (Variation ID: 1758684). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of 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: Nov 3, 2024

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