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NM_000051.4(ATM):c.4060C>A (p.Pro1354Thr) AND ATM-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 27, 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:
RCV004549549.1

Allele description [Variation Report for NM_000051.4(ATM):c.4060C>A (p.Pro1354Thr)]

NM_000051.4(ATM):c.4060C>A (p.Pro1354Thr)

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.4060C>A (p.Pro1354Thr)
Other names:
p.P1354T:CCA>ACA
HGVS:
  • NC_000011.10:g.108287666C>A
  • NG_009830.1:g.69835C>A
  • NM_000051.4:c.4060C>AMANE SELECT
  • NM_001351834.2:c.4060C>A
  • NP_000042.3:p.Pro1354Thr
  • NP_000042.3:p.Pro1354Thr
  • NP_001338763.1:p.Pro1354Thr
  • LRG_135t1:c.4060C>A
  • LRG_135:g.69835C>A
  • LRG_135p1:p.Pro1354Thr
  • NC_000011.9:g.108158393C>A
  • NM_000051.3:c.4060C>A
  • p.P1354T
Protein change:
P1354T
Links:
dbSNP: rs145119475
NCBI 1000 Genomes Browser:
rs145119475
Molecular consequence:
  • NM_000051.4:c.4060C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.4060C>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
SCV000805552PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 27, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV000805552.3

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

Description

The ATM c.4060C>A variant is predicted to result in the amino acid substitution p.Pro1354Thr. This variant has been reported in individuals with a personal history of cancer (Lu et al. 2015. PubMed ID: 26689913, supplementary data 12) and has also been reported in an equal numbers of breast cancer cases and controls (Tavtigian et al. 2009. Table S2. PubMed ID: 19781682). In two other large cancer cohort studies, this variant was reported as a variant of uncertain significance (Quezada Urban et al. 2018. PubMed ID: 30262796, Supplementary Table 2; Fanale et al. 2020. PubMed ID: 32854451). It has been reported at frequencies up to ~0.04% in a large population database and has conflicting interpretations in ClinVar ranging from benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/127379/). Although we suspect that this variant could be benign, at this time, its clinical significance is classified as uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Jun 17, 2024