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NM_000051.4(ATM):c.7789G>T (p.Asp2597Tyr) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 10, 2022
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:
RCV002406516.9

Allele description [Variation Report for NM_000051.4(ATM):c.7789G>T (p.Asp2597Tyr)]

NM_000051.4(ATM):c.7789G>T (p.Asp2597Tyr)

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.7789G>T (p.Asp2597Tyr)
HGVS:
  • NC_000011.10:g.108332762G>T
  • NG_009830.1:g.114931G>T
  • NG_054724.1:g.142071C>A
  • NM_000051.4:c.7789G>TMANE SELECT
  • NM_001330368.2:c.641-23691C>A
  • NM_001351110.2:c.*38+2458C>A
  • NM_001351834.2:c.7789G>T
  • NP_000042.3:p.Asp2597Tyr
  • NP_000042.3:p.Asp2597Tyr
  • NP_001338763.1:p.Asp2597Tyr
  • LRG_135t1:c.7789G>T
  • LRG_135:g.114931G>T
  • LRG_135p1:p.Asp2597Tyr
  • NC_000011.9:g.108203489G>T
  • NM_000051.3:c.7789G>T
Protein change:
D2597Y
Links:
dbSNP: rs1555125212
NCBI 1000 Genomes Browser:
rs1555125212
Molecular consequence:
  • NM_001330368.2:c.641-23691C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*38+2458C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.7789G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.7789G>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002669051Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Feb 10, 2022) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

ATM germline mutations in women with familial breast cancer and a relative with haematological malignancy.

Paglia LL, Laugé A, Weber J, Champ J, Cavaciuti E, Russo A, Viovy JL, Stoppa-Lyonnet D.

Breast Cancer Res Treat. 2010 Jan;119(2):443-52. doi: 10.1007/s10549-009-0396-z. Epub 2009 Apr 29.

PubMed [citation]
PMID:
19404735

Details of each submission

From Ambry Genetics, SCV002669051.2

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

Description

The c.7789G>T variant (also known as p.D2597Y) is located in coding exon 52 of the ATM gene. This alteration was identified in 1/122 BRCA1/2-negative women with a personal history of breast cancer and a family history of both breast cancer and hematological malignancy (Paglia LL et al. Breast Cancer Res Treat, 2010 Jan;119:443-52). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site. A published RNA study reported that this variant causes skipping of coding exon 52 (Paglia LL et al. Breast Cancer Res Treat, 2010 Jan;119:443-52). Internal RNA studies have also demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: Nov 10, 2024