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NM_000051.4(ATM):c.6095G>A (p.Arg2032Lys) AND ATM-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 15, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004551374.3

Allele description [Variation Report for NM_000051.4(ATM):c.6095G>A (p.Arg2032Lys)]

NM_000051.4(ATM):c.6095G>A (p.Arg2032Lys)

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.6095G>A (p.Arg2032Lys)
Other names:
p.R2032K:AGA>AAA
HGVS:
  • NC_000011.10:g.108315911G>A
  • NG_009830.1:g.98080G>A
  • NG_054724.1:g.158922C>T
  • NM_000051.4:c.6095G>AMANE SELECT
  • NM_001330368.2:c.641-6840C>T
  • NM_001351110.2:c.*39-6840C>T
  • NM_001351834.2:c.6095G>A
  • NP_000042.3:p.Arg2032Lys
  • NP_000042.3:p.Arg2032Lys
  • NP_001338763.1:p.Arg2032Lys
  • LRG_135t1:c.6095G>A
  • LRG_135:g.98080G>A
  • LRG_135p1:p.Arg2032Lys
  • NC_000011.9:g.108186638G>A
  • NM_000051.3:c.6095G>A
  • p.R2032K
Protein change:
R2032K
Links:
dbSNP: rs139770721
NCBI 1000 Genomes Browser:
rs139770721
Molecular consequence:
  • NM_001330368.2:c.641-6840C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*39-6840C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.6095G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.6095G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
ATM-related disorder
Synonyms:
ATM-related disorders; ATM-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004732114PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Dec 15, 2023) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004732114.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The ATM c.6095G>A variant is predicted to result in the amino acid substitution p.Arg2032Lys. Of note, this variant occurs at the last nucleotide of the exon and is predicted to significantly weaken the donor splice site (Alamut Visual Plus v1.6.1) and exon skipping was observed in analyses from patient lymphocytes (Sandoval et al 1999. PubMed ID: 9887333). This variant has been observed in the compound heterozygous or homozygous state in individuals with ataxia telangiectasia (Sandoval. 1999. PubMed ID: 9887333; Teraoka et al. 1999. PubMed ID: 10330348; Mitui et al. 2005. PubMed ID: 16266405). The c.6095G>A variant has also been reported in the heterozygous state in several individuals with pancreatic cancer, gastric cancer, prostate cancer, and breast cancer (Roberts et al. 2012. PubMed ID: 22585167; Huang et al. 2015. PubMed ID: 26506520; Table 1, Wokołorczyk D et al 2020. PubMed ID: 32875559; Schubert S et al 2019. PubMed ID: 30426508). This variant was reported as a germline variant in a patient with chronic lymphocytic leukemia (Table S2. Petrackova et al. 2022. PubMed ID: 36029002). This variant is reported in 0.0062% of alleles in individuals of European (Non-Finnish) descent in gnomAD. In ClinVar, this variant is reported as likely pathogenic and pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/181974/). This variant is interpreted as pathogenic.

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

Last Updated: Oct 13, 2024