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NM_000051.4(ATM):c.1564_1565del (p.Glu522fs) AND ATM-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 22, 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:
RCV004549540.2

Allele description

NM_000051.4(ATM):c.1564_1565del (p.Glu522fs)

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.1564_1565del (p.Glu522fs)
HGVS:
  • NC_000011.10:g.108251027GA[1]
  • NG_009830.1:g.33196GA[1]
  • NM_000051.4:c.1564_1565delMANE SELECT
  • NM_001351834.2:c.1564_1565del
  • NP_000042.3:p.Glu522fs
  • NP_001338763.1:p.Glu522fs
  • LRG_135:g.33196GA[1]
  • NC_000011.9:g.108121753_108121754del
  • NC_000011.9:g.108121754GA[1]
  • NM_000051.3:c.1561_1562delAG
  • NM_000051.3:c.1564_1565delGA
  • NM_000051.4:c.1564_1565del
  • NM_000051.4:c.1564_1565delGAMANE SELECT
  • c.1563delAG
  • c.1564_1565delGA
  • p.E522IFS*43
  • p.E522IfsX43
  • p.Glu522IlefsTer43
  • p.Glu522IlefsX43
Protein change:
E522fs
Links:
dbSNP: rs587779817
NCBI 1000 Genomes Browser:
rs587779817
Molecular consequence:
  • NM_000051.4:c.1564_1565del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351834.2:c.1564_1565del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004732468PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 22, 2024) 		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, SCV004732468.1

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

Description

The ATM c.1564_1565delGA variant is predicted to result in a frameshift and premature protein termination (p.Glu522Ilefs*43). This variant has previously been reported in patients with ataxia telangiectasia (Byrd et al. 1996. PubMed ID: 8789452), as well as in individuals with a personal or family history of breast, pancreatic, gastric, and colorectal cancers (Decker et al. 2017. PubMed ID: 28779002; Hansford et al. 2015. PubMed ID: 26182300; Huang et al. 2015. PubMed ID: 26506520; Shindo et al. 2017. PubMed ID: 28767289; Tung et al. 2014. PubMed ID: 25186627; Yurgelun et al. 2015. PubMed ID: 25980754). This variant is reported in 0.011% of alleles in individuals of European (Non-Finnish) descent in gnomAD and is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/127340/). Frameshift variants in ATM are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Sep 29, 2024