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NM_000051.4(ATM):c.3049C>T (p.Gln1017Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 28, 2021)
Last evaluated:
Sep 11, 2020
Accession:
VCV000181992.10
Variation ID:
181992
Description:
single nucleotide variant
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NM_000051.4(ATM):c.3049C>T (p.Gln1017Ter)

Allele ID
180433
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108271378 (GRCh38) GRCh38 UCSC
11: 108142105 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.108271378C>T
NG_009830.1:g.53547C>T
NM_000051.4:c.3049C>T MANE Select NP_000042.3:p.Gln1017Ter nonsense
... more HGVS
Protein change
Q1017*
Other names
p.Q1017*:CAG>TAG
Canonical SPDI
NC_000011.10:108271377:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA298345
dbSNP: rs730881388
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Sep 11, 2020 RCV000457084.7
Pathogenic 1 criteria provided, single submitter Jul 2, 2018 RCV000159761.5
Pathogenic 1 criteria provided, single submitter Jun 10, 2020 RCV000211992.3
Likely pathogenic 1 criteria provided, single submitter Oct 8, 2018 RCV001258064.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATM Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
6418 10309

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 02, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000216002.5
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The p.Q1017* pathogenic mutation (also known as c.3049C>T), located in coding exon 19 of the ATM gene, results from a C to T substitution at … (more)
Pathogenic
(Jun 10, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000209780.11
Submitted: (Sep 28, 2021)
Evidence details
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Pathogenic
(Oct 28, 2019)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694246.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: ATM c.3049C>T (p.Gln1017X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Likely pathogenic
(Oct 08, 2018)
criteria provided, single submitter
Method: clinical testing
Susceptibility to breast cancer
Ataxia-telangiectasia
Allele origin: germline
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Accession: SCV001434895.1
Submitted: (Apr 23, 2020)
Evidence details
Comment:
The c.3049C>T (p.Gln1017*) variant in the ATM gene is predicted to introduce a premature translation termination codon. This variant has not been reported in the … (more)
Pathogenic
(Sep 11, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000546762.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Gln1017*) in the ATM gene. It is expected to result in an absent or disrupted protein … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing. Susswein LR Genetics in medicine : official journal of the American College of Medical Genetics 2016 PMID: 26681312
Ten new ATM alterations in Polish patients with ataxia-telangiectasia. Podralska MJ Molecular genetics & genomic medicine 2014 PMID: 25614872
Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients. Huang Y Neuromolecular medicine 2013 PMID: 23807571

Text-mined citations for rs730881388...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021