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NM_000051.4(ATM):c.1931C>A (p.Ser644Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jun 11, 2021)
Last evaluated:
Sep 28, 2020
Accession:
VCV000233607.8
Variation ID:
233607
Description:
single nucleotide variant
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NM_000051.4(ATM):c.1931C>A (p.Ser644Ter)

Allele ID
234008
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108124573 (GRCh37) GRCh37 UCSC
11: 108253846 (GRCh38) GRCh38 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_135:g.36015C>A
LRG_135t1:c.1931C>A LRG_135p1:p.Ser644Ter
NC_000011.9:g.108124573C>A
... more HGVS
Protein change
S644*
Other names
-
Canonical SPDI
NC_000011.10:108253845:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10579032
dbSNP: rs768362387
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 28, 2020 RCV000222313.2
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jan 29, 2020 RCV000576759.5
Pathogenic 1 criteria provided, single submitter Jun 8, 2017 RCV000482158.1
Pathogenic 1 criteria provided, single submitter Oct 31, 2018 RCV000762815.1
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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
6424 10317

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jun 08, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000568316.5
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted ATM c.1931C>A at the cDNA level and p.Ser644Ter (S644X) at the protein level. The substitution creates a nonsense variant, which changes … (more)
Pathogenic
(Sep 25, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000278014.5
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The p.S644* pathogenic mutation (also known as c.1931C>A), located in coding exon 12 of the ATM gene, results from a C to A substitution at … (more)
Likely pathogenic
(Jun 14, 2017)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: unknown
Counsyl
Accession: SCV000678107.1
Submitted: (Jun 22, 2017)
Evidence details
Publications
PubMed (1)
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Familial cancer of breast
Ataxia-telangiectasia syndrome
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893173.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Jan 29, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000825216.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change creates a premature translational stop signal (p.Ser644*) in the ATM gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Sep 28, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV001734339.1
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This variant changes 1 nucleotide in exon 13 of the ATM gene, creating a premature translation stop signal. This variant is expected to result in … (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
Loss-of-function variants in ATM confer risk of gastric cancer. Helgason H Nature genetics 2015 PMID: 26098866
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Prevalence of germline mutations in cancer predisposition genes in patients with pancreatic cancer. Grant RC Gastroenterology 2015 PMID: 25479140
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
Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer. Grant RC Human genomics 2013 PMID: 23561644
Mutations at the ataxia-telangiectasia locus and clinical phenotypes of A-T patients. Li A American journal of medical genetics 2000 PMID: 10817650

Text-mined citations for rs768362387...

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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 Dec 04, 2021