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NM_000051.4(ATM):c.5573G>A (p.Trp1858Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Apr 19, 2020
Accession:
VCV000246068.7
Variation ID:
246068
Description:
single nucleotide variant
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NM_000051.4(ATM):c.5573G>A (p.Trp1858Ter)

Allele ID
244621
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108304751 (GRCh38) GRCh38 UCSC
11: 108175478 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_135:g.86920G>A
LRG_135t1:c.5573G>A LRG_135p1:p.Trp1858Ter
NC_000011.9:g.108175478G>A
... more HGVS
Protein change
W1858*
Other names
-
Canonical SPDI
NC_000011.10:108304750:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10584352
dbSNP: rs879254076
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Apr 19, 2020 RCV000628037.7
Pathogenic 1 criteria provided, single submitter Jan 16, 2017 RCV000236378.1
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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
(Jan 16, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000293377.9
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This pathogenic variant is denoted ATM c.5573G>A at the cDNA level and p.Trp1858Ter (W1858X) at the protein level. The substitution creates a nonsense variant, which … (more)
Likely pathogenic
(Apr 14, 2017)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: unknown
Counsyl
Accession: SCV000790919.1
Submitted: (Jul 10, 2018)
Evidence details
Pathogenic
(Jun 13, 2019)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
(Autosomal recessive inheritance)
Allele origin: paternal
Institute of Human Genetics, Klinikum rechts der Isar
Accession: SCV001150022.1
Submitted: (Jan 21, 2020)
Evidence details
Pathogenic
(Apr 19, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000748925.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Trp1858*) 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
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
ATM protein and p53-serine 15 phosphorylation in ataxia-telangiectasia (AT) patients and at heterozygotes. Delia D British journal of cancer 2000 PMID: 10864201

Text-mined citations for rs879254076...

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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