NM_000051.4(ATM):c.7921C>T (p.Gln2641Ter) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Apr 15, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000657754.14

Allele description [Variation Report for NM_000051.4(ATM):c.7921C>T (p.Gln2641Ter)]

NM_000051.4(ATM):c.7921C>T (p.Gln2641Ter)

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.7921C>T (p.Gln2641Ter)

HGVS:

NC_000011.10:g.108332894C>T
NG_009830.1:g.115063C>T
NG_054724.1:g.141939G>A
NM_000051.4:c.7921C>TMANE SELECT
NM_001330368.2:c.641-23823G>A
NM_001351110.2:c.*38+2326G>A
NM_001351834.2:c.7921C>T
NP_000042.3:p.Gln2641Ter
NP_000042.3:p.Gln2641Ter
NP_001338763.1:p.Gln2641Ter
LRG_135t1:c.7921C>T
LRG_135:g.115063C>T
LRG_135p1:p.Gln2641Ter
NC_000011.9:g.108203621C>T
NM_000051.3:c.7921C>T

Protein change:

Q2641*

Links:

dbSNP: rs769523686

NCBI 1000 Genomes Browser:

rs769523686

Molecular consequence:

NM_001330368.2:c.641-23823G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+2326G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.7921C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351834.2:c.7921C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000779506	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Apr 15, 2022)	germline	clinical testing	Citation Link,
SCV002069108	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 8, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000779506

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Apr 15, 2022)

germline

clinical testing

Citation Link,

SCV002069108

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 8, 2018)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 GeneDx, SCV000779506.3

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Observed in men with prostate cancer (Nguyen-Dumont 2020, Darst 2021, Karlsson 2021); This variant is associated with the following publications: (PMID: 22980975, 32338768, 33436325, 32853339)

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

From Genetic Services Laboratory, University of Chicago, SCV002069108.1

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

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

Last Updated: Nov 10, 2024

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