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NM_000051.4(ATM):c.6082del (p.Gln2028fs) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Dec 27, 2021
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:
RCV000755037.11

Allele description [Variation Report for NM_000051.4(ATM):c.6082del (p.Gln2028fs)]

NM_000051.4(ATM):c.6082del (p.Gln2028fs)

Genes:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.6082del (p.Gln2028fs)
Other names:
p.Gln2028AsnfsTer19
HGVS:
  • NC_000011.10:g.108315898del
  • NG_009830.1:g.98067del
  • NG_054724.1:g.158935del
  • NM_000051.4:c.6082delMANE SELECT
  • NM_001330368.2:c.641-6827del
  • NM_001351110.2:c.*39-6827del
  • NM_001351834.2:c.6082del
  • NP_000042.3:p.Gln2028Asnfs
  • NP_000042.3:p.Gln2028fs
  • NP_001338763.1:p.Gln2028fs
  • LRG_135t1:c.6082del
  • LRG_135:g.98067del
  • NC_000011.9:g.108186625del
  • NM_000051.3:c.6082del
  • NM_000051.3:c.6082delC
Protein change:
Q2028fs
Links:
dbSNP: rs1565499093
NCBI 1000 Genomes Browser:
rs1565499093
Molecular consequence:
  • NM_000051.4:c.6082del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351834.2:c.6082del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330368.2:c.641-6827del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*39-6827del - intron variant - [Sequence Ontology: SO:0001627]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000882857Department of Molecular Diagnostics, Institute of Oncology Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 24, 2018)
germlineclinical testing

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

SCV002657980Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Pathogenic
(Dec 27, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
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 Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SCV000882857.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Ambry Genetics, SCV002657980.2

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

Description

The c.6082delC pathogenic mutation, located in coding exon 40 of the ATM gene, results from a deletion of one nucleotide at nucleotide position 6082, causing a translational frameshift with a predicted alternate stop codon (p.Q2028Nfs*19). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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

Last Updated: Feb 1, 2025