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NM_000051.4(ATM):c.689del (p.Asn230fs) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Sep 6, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001025773.6

Allele description [Variation Report for NM_000051.4(ATM):c.689del (p.Asn230fs)]

NM_000051.4(ATM):c.689del (p.Asn230fs)

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.689del (p.Asn230fs)
HGVS:
  • NC_000011.10:g.108244814del
  • NG_009830.1:g.26983del
  • NM_000051.4:c.689delMANE SELECT
  • NM_001351834.2:c.689del
  • NP_000042.3:p.Asn230fs
  • NP_000042.3:p.Asn230fs
  • NP_001338763.1:p.Asn230fs
  • LRG_135t1:c.689del
  • LRG_135:g.26983del
  • LRG_135p1:p.Asn230fs
  • NC_000011.9:g.108115539del
  • NC_000011.9:g.108115541del
  • NM_000051.3:c.687delA
  • NM_000051.3:c.689del
  • NM_000051.3:c.689del
  • NM_000051.3:c.689delA
  • NM_000051.3:c.689delA
Protein change:
N230fs
Links:
dbSNP: rs1057518965
NCBI 1000 Genomes Browser:
rs1057518965
Molecular consequence:
  • NM_000051.4:c.689del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351834.2:c.689del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001188025Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Sep 6, 2023) 		germlineclinical testing

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

Citation Link,

SCV002538561Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)		Likely pathogenic
(Nov 4, 2021) 		germlinecuration

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Contributions of ATM mutations to familial breast and ovarian cancer.

Thorstenson YR, Roxas A, Kroiss R, Jenkins MA, Yu KM, Bachrich T, Muhr D, Wayne TL, Chu G, Davis RW, Wagner TM, Oefner PJ.

Cancer Res. 2003 Jun 15;63(12):3325-33.

PubMed [citation]
PMID:
12810666

Functional classification of ATM variants in ataxia-telangiectasia patients.

Fiévet A, Bellanger D, Rieunier G, Dubois d'Enghien C, Sophie J, Calvas P, Carriere JP, Anheim M, Castrioto A, Flabeau O, Degos B, Ewenczyk C, Mahlaoui N, Touzot F, Suarez F, Hully M, Roubertie A, Aladjidi N, Tison F, Antoine-Poirel H, Dahan K, Doummar D, et al.

Hum Mutat. 2019 Oct;40(10):1713-1730. doi: 10.1002/humu.23778. Epub 2019 May 17.

PubMed [citation]
PMID:
31050087

Details of each submission

From Ambry Genetics, SCV001188025.5

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

Description

The c.689delA pathogenic mutation, located in coding exon 6 of the ATM gene, results from a deletion of one nucleotide at nucleotide position 689, causing a translational frameshift with a predicted alternate stop codon (p.N230Ifs*4). This mutation, designated 687delA, was identified in an Austrian family with three or more affected individuals, including two diagnosed with breast cancer before age 50 (Thorstenson YR et al. Cancer Res. 2003 Jun;63:3325-33). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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

From Sema4, Sema4, SCV002538561.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024