NM_000051.3(ATM):c.1564_1565delGA (p.Glu522Ilefs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Aug 29, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description

NM_000051.3(ATM):c.1564_1565delGA (p.Glu522Ilefs)

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_000051.3(ATM):c.1564_1565delGA (p.Glu522Ilefs)
  • NC_000011.10:g.108251029_108251030delGA
  • NP_000042.3:p.Glu522Ilefs
  • LRG_135t1:c.1564_1565del
  • LRG_135:g.33198_33199del
  • LRG_135p1:p.Glu522Ilefs
  • NC_000011.9:g.108121756_108121757delGA
  • NM_000051.3:c.1561_1562delAG
  • NM_000051.3:c.1564_1565delGA
  • c.1563delAG
  • c.1564_1565delGA
  • p.E522IFS*43
  • p.E522IfsX43
  • p.Glu522IlefsTer43
  • p.Glu522IlefsX43
dbSNP: rs587779817
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000051.3:c.1564_1565delGA - frameshift variant - [Sequence Ontology: SO:0001589]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000149053GeneDxcriteria provided, single submitter
(Apr 17, 2017)
germlineclinical testing

Citation Link,

SCV000610563Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicscriteria provided, single submitter
(Aug 29, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing



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]

Details of each submission

From GeneDx, SCV000149053.13

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


The ATM c.1564_1565delGA deletion causes a frameshift, which changes a Glutamic Acid to an Isoleucine at codon 522, and creates a premature stop codon at position 43 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. ATM c.1564_1565delGA, also reported as c.1563_1564delAG and c.1561_1562delAG, has been observed in individuals with recessively inherited Ataxia-telangiectasia and in patients with breast cancer, gastric cancer, and an unspecified Lynch syndrome-related cancer and/or polyps (Byrd 1996, Demuth 2011, Verhagen 2012, Driessen 2013, Huang 2015, Hansford 2015, Yurgelun 2015, Mansfield 2016). We consider this variant to be pathogenic.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics, SCV000610563.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.000208not providednot provided

Last Updated: Mar 30, 2019

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