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NM_000051.4(ATM):c.5932G>T (p.Glu1978Ter) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 19, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001258122.9

Allele description [Variation Report for NM_000051.4(ATM):c.5932G>T (p.Glu1978Ter)]

NM_000051.4(ATM):c.5932G>T (p.Glu1978Ter)

Genes:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.5932G>T (p.Glu1978Ter)
Other names:
p.E1978*:GAA>TAA
HGVS:
  • NC_000011.10:g.108312424G>T
  • NG_009830.1:g.94593G>T
  • NG_054724.1:g.162409C>A
  • NM_000051.4:c.5932G>TMANE SELECT
  • NM_001330368.2:c.641-3353C>A
  • NM_001351110.2:c.*39-3353C>A
  • NM_001351834.2:c.5932G>T
  • NP_000042.3:p.Glu1978Ter
  • NP_000042.3:p.Glu1978Ter
  • NP_001338763.1:p.Glu1978Ter
  • LRG_135t1:c.5932G>T
  • LRG_135:g.94593G>T
  • LRG_135p1:p.Glu1978Ter
  • NC_000011.9:g.108183151G>T
  • NM_000051.3:c.5932G>T
  • p.E1978*
  • p.Glu1978Stop
Protein change:
E1978*
Links:
dbSNP: rs587779852
NCBI 1000 Genomes Browser:
rs587779852
Molecular consequence:
  • NM_001330368.2:c.641-3353C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*39-3353C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.5932G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351834.2:c.5932G>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
Name:
Breast cancer, susceptibility to
Identifiers:
MedGen: C3469522

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001434995Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Dec 19, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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 Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine, SCV001434995.1

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

Description

This c.5932G>T (p.Glu1978Ter) variant in exon 41 of the ATM gene creates a premature translational stop signal and is predicted to result in loss of function through nonsense-mediated mRNA decay or by producing a truncated protein. This variant is present in population databases (rs587779852, gnomAD 0.004379%). This variant has been reported in several individuals affected with ataxia-telangiectasia (PMID: 15880721, 16266405, 17124347, 18497957, 19691550, 25614872) and breast cancer (PMID: 18807267). It has been found to be a prevalent ATM mutation in Eastern Europe (PMID: 15880721, 16266405, 18807267). Experimental studies indicate that this nonsense change leads to out-of-frame skipping of exon 41 (PMID: 10330348, 24451234). Therefore, this variant is classified as pathogenic.

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

Last Updated: Nov 3, 2024