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NM_000051.4(ATM):c.2839-1G>A AND Ataxia-telangiectasia syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 3, 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:
RCV001961473.5

Allele description

NM_000051.4(ATM):c.2839-1G>A

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.2839-1G>A
HGVS:
  • NC_000011.10:g.108271063G>A
  • NG_009830.1:g.53232G>A
  • NM_000051.4:c.2839-1G>AMANE SELECT
  • NM_001351834.2:c.2839-1G>A
  • LRG_135:g.53232G>A
  • NC_000011.9:g.108141790G>A
Links:
dbSNP: rs995271490
NCBI 1000 Genomes Browser:
rs995271490
Molecular consequence:
  • NM_000051.4:c.2839-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001351834.2:c.2839-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002252438Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 3, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Ataxia-telangiectasia: phenotype/genotype studies of ATM protein expression, mutations, and radiosensitivity.

Becker-Catania SG, Chen G, Hwang MJ, Wang Z, Sun X, Sanal O, Bernatowska-Matuszkiewicz E, Chessa L, Lee EY, Gatti RA.

Mol Genet Metab. 2000 Jun;70(2):122-33.

PubMed [citation]
PMID:
10873394

Comprehensive scanning of the ATM gene with DOVAM-S.

Buzin CH, Gatti RA, Nguyen VQ, Wen CY, Mitui M, Sanal O, Chen JS, Nozari G, Mengos A, Li X, Fujimura F, Sommer SS.

Hum Mutat. 2003 Feb;21(2):123-31.

PubMed [citation]
PMID:
12552559
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV002252438.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 18 of the ATM gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in the loss of 6 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. ClinVar contains an entry for this variant (Variation ID: 1469238). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the ATM protein in which other variant(s) (p.Leu950Arg) have been determined to be pathogenic (PMID: 10873394, 12552559, 20678261, 21792198, 27989354). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. Studies have shown that disruption of this splice site results in the activation of a cryptic splice site in exon 19 (Invitae).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024