NM_000051.4(ATM):c.7327C>T (p.Arg2443Ter) AND not provided

Germline classification:: Pathogenic (5 submissions)
Last evaluated:: Nov 22, 2023
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:: RCV000484232.40

Allele description [Variation Report for NM_000051.4(ATM):c.7327C>T (p.Arg2443Ter)]

NM_000051.4(ATM):c.7327C>T (p.Arg2443Ter)

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.7327C>T (p.Arg2443Ter)

HGVS:

NC_000011.10:g.108330233C>T
NG_009830.1:g.112402C>T
NG_054724.1:g.144600G>A
NM_000051.4:c.7327C>TMANE SELECT
NM_001330368.2:c.641-21162G>A
NM_001351110.2:c.*38+4987G>A
NM_001351834.2:c.7327C>T
NP_000042.3:p.Arg2443Ter
NP_000042.3:p.Arg2443Ter
NP_001338763.1:p.Arg2443Ter
LRG_135t1:c.7327C>T
LRG_135:g.112402C>T
LRG_135p1:p.Arg2443Ter
NC_000011.9:g.108200960C>T
NM_000051.3:c.7327C>T
NM_001351834.2:c.7327C>T

Protein change:

R2443*; ARG2443TER

Links:

OMIM: 607585.0019; dbSNP: rs121434220

NCBI 1000 Genomes Browser:

rs121434220

Molecular consequence:

NM_001330368.2:c.641-21162G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+4987G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.7327C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351834.2:c.7327C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

BB278168 RIKEN full-length enriched, adult retina Mus musculus cDNA clone A93000...
BB278168 RIKEN full-length enriched, adult retina Mus musculus cDNA clone A930009L07 3', mRNA sequence
gi|16401051|gnl|dbEST|9996986|dbj|B 68.2|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566496	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Feb 17, 2023)	germline	clinical testing	Citation Link,
SCV000805612	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 14, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001246116	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Dec 1, 2020)	germline	clinical testing	Citation Link,
SCV001447181	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004167632	Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg	criteria provided, single submitter (Hauer et al. (Genet Med. 2018))	Pathogenic (Nov 22, 2023)	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	4	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	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

Clinical relevance of systematic phenotyping and exome sequencing in patients with short stature.

Hauer NN, Popp B, Schoeller E, Schuhmann S, Heath KE, Hisado-Oliva A, Klinger P, Kraus C, Trautmann U, Zenker M, Zweier C, Wiesener A, Abou Jamra R, Kunstmann E, Wieczorek D, Uebe S, Ferrazzi F, Büttner C, Ekici AB, Rauch A, Sticht H, Dörr HG, et al.

Genet Med. 2018 Jun;20(6):630-638. doi: 10.1038/gim.2017.159. Epub 2017 Oct 12.

PubMed [citation]

PMID:: 29758562
PMCID:: PMC5993671

Details of each submission

From GeneDx, SCV000566496.5

#	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; Observed as heterozygous in individuals with personal or family cancer history consistent with pathogenic variants in this gene referred for genetic testing at GeneDx and in published literature (Leongamornlert et al., 2014, Hu et al., 2016, Lhota et al., 2016, Resch et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 19440741, 21833744, 29922827, 24556621, 9443866, 25525159, 15101044, 12497634, 26822949, 28059096, 26483394, 28984303, 12673797, 10817650, 8808599, 9887333, 12697903, 17203191, 29522266, 30322717, 28888541, 33436325, 34680878, 30198223)

#	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 PreventionGenetics, part of Exact Sciences, SCV000805612.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001246116.26

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

#	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		3	not provided	not provided	not provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001447181.1

#	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	1	not provided	not provided		not provided	not provided	not provided	not provided

From Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, SCV004167632.1

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

Description

This variant has been identified by standard clinical testing. female patient with triple-negative breast cancer Selected ACMG criteria: Pathogenic (I):PP5;PM2;PVS1

#	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		1	not provided	not provided	not provided

Last Updated: Nov 3, 2024

ClinVar

Relating variation to medicine