NM_000051.4(ATM):c.1931C>A (p.Ser644Ter) AND Malignant tumor of breast

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 30, 2023
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:: RCV003235146.1

Allele description [Variation Report for NM_000051.4(ATM):c.1931C>A (p.Ser644Ter)]

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

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.1931C>A (p.Ser644Ter)

HGVS:

NC_000011.10:g.108253846C>A
NG_009830.1:g.36015C>A
NM_000051.4:c.1931C>AMANE SELECT
NM_001351834.2:c.1931C>A
NP_000042.3:p.Ser644Ter
NP_000042.3:p.Ser644Ter
NP_001338763.1:p.Ser644Ter
LRG_135t1:c.1931C>A
LRG_135:g.36015C>A
LRG_135p1:p.Ser644Ter
NC_000011.9:g.108124573C>A
NM_000051.3:c.1931C>A

Protein change:

S644*

Links:

dbSNP: rs768362387

NCBI 1000 Genomes Browser:

rs768362387

Molecular consequence:

NM_000051.4:c.1931C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001351834.2:c.1931C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Malignant tumor of breast
Synonyms:: Malignant breast neoplasm; Cancer breast
Identifiers:: MONDO: MONDO:0007254; MedGen: C0006142

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UI-H-BI0-aae-a-10-0-UI.s1 NCI_CGAP_Sub1 Homo sapiens cDNA clone IMAGE:2709018 3'...
UI-H-BI0-aae-a-10-0-UI.s1 NCI_CGAP_Sub1 Homo sapiens cDNA clone IMAGE:2709018 3', mRNA sequence
gi|5863476|gnl|dbEST|3143707|gb|AW0 .1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003934459	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (May 30, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003934459

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(May 30, 2023)

germline

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations at the ataxia-telangiectasia locus and clinical phenotypes of A-T patients.

Li A, Swift M.

Am J Med Genet. 2000 May 29;92(3):170-7.

PubMed [citation]

PMID:: 10817650

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003934459.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Variant summary: ATM c.1931C>A (p.Ser644X) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, which is a commonly known mechanisms for disease. Another variant resulting in the same termination codon is classified as pathogenic in ClinVar (c.1931C>G). The variant was absent in 251128 control chromosomes (gnomAD). c.1931C>A has been reported in the literature in compound heterozygous individual(s) affected with Ataxia-Telangiectasia (Li_2000). The following publication has been ascertained in the context of this evaluation (PMID: 10817650). Six submitters have provided clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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