NM_000051.4(ATM):c.877A>T (p.Lys293Ter) AND Ataxia-telangiectasia syndrome

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Feb 28, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000411113.2

Allele description [Variation Report for NM_000051.4(ATM):c.877A>T (p.Lys293Ter)]

NM_000051.4(ATM):c.877A>T (p.Lys293Ter)

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.877A>T (p.Lys293Ter)
HGVS:
  • NC_000011.10:g.108245002A>T
  • NG_009830.1:g.27171A>T
  • NM_000051.3:c.877A>T
  • NM_000051.4:c.877A>TMANE SELECT
  • NM_001351834.2:c.877A>T
  • NP_000042.3:p.Lys293Ter
  • NP_000042.3:p.Lys293Ter
  • NP_001338763.1:p.Lys293Ter
  • LRG_135t1:c.877A>T
  • LRG_135:g.27171A>T
  • LRG_135p1:p.Lys293Ter
  • NC_000011.9:g.108115729A>T
Protein change:
K293*
Links:
dbSNP: rs1057516442
NCBI 1000 Genomes Browser:
rs1057516442
Molecular consequence:
  • NM_000051.3:c.877A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000051.4:c.877A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351834.2:c.877A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Ataxia-telangiectasia syndrome (AT)
Synonyms:
Louis-Bar syndrome; Cerebello-oculocutaneous telangiectasia; Immunodeficiency with ataxia telangiectasia; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008840; MedGen: C0004135; Orphanet: 100; OMIM: 208900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000485684Counsylcriteria provided, single submitter
Likely pathogenic
(Jan 27, 2016)
unknownclinical testing

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

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV001585448Invitaecriteria provided, single submitter
Pathogenic
(Feb 28, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

ATM mutations uniformly lead to ATM dysfunction in chronic lymphocytic leukemia: application of functional test using doxorubicin.

Navrkalova V, Sebejova L, Zemanova J, Kminkova J, Kubesova B, Malcikova J, Mraz M, Smardova J, Pavlova S, Doubek M, Brychtova Y, Potesil D, Nemethova V, Mayer J, Pospisilova S, Trbusek M.

Haematologica. 2013 Jul;98(7):1124-31. doi: 10.3324/haematol.2012.081620. Epub 2013 Apr 12.

PubMed [citation]
PMID:
23585524
PMCID:
PMC3696617

Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients.

Huang Y, Yang L, Wang J, Yang F, Xiao Y, Xia R, Yuan X, Yan M.

Neuromolecular Med. 2013 Sep;15(3):536-40. doi: 10.1007/s12017-013-8240-3. Epub 2013 Jun 27. Erratum in: Neuromolecular Med. 2014 Mar;16(1):216.

PubMed [citation]
PMID:
23807571
PMCID:
PMC3732755
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000485684.1

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

From Invitae, SCV001585448.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Lys293*) in the ATM gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with ATM-related conditions. ClinVar contains an entry for this variant (Variation ID: 370378). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 30, 2021

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