NM_000051.4(ATM):c.6177dup (p.Arg2060fs) AND ATM-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 21, 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:: RCV004549887.1

Allele description [Variation Report for NM_000051.4(ATM):c.6177dup (p.Arg2060fs)]

NM_000051.4(ATM):c.6177dup (p.Arg2060fs)

Genes:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]

Variant type:

Duplication

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.6177dup (p.Arg2060fs)

HGVS:

NC_000011.10:g.108316092dup
NG_009830.1:g.98261dup
NG_054724.1:g.158741dup
NM_000051.4:c.6177dupMANE SELECT
NM_001330368.2:c.641-7021dup
NM_001351110.2:c.*39-7021dup
NM_001351834.2:c.6177dup
NP_000042.3:p.Arg2060Thrfs
NP_000042.3:p.Arg2060fs
NP_001338763.1:p.Arg2060fs
LRG_135t1:c.6177dup
LRG_135:g.98261dup
LRG_135p1:p.Arg2060Thrfs
NC_000011.9:g.108186818_108186819insA
NC_000011.9:g.108186819dup
NM_000051.3:c.6177dup
NM_000051.3:c.6177dupA

Protein change:

R2060fs

Links:

dbSNP: rs1591779373

NCBI 1000 Genomes Browser:

rs1591779373

Molecular consequence:

NM_000051.4:c.6177dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001351834.2:c.6177dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330368.2:c.641-7021dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-7021dup - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: ATM-related disorder
Synonyms:: ATM-related disorders; ATM-related condition
Identifiers:

Recent activity

Clear Turn Off Turn On

Homo sapiens calcium responsive transcription factor (CARF), transcript variant ...
Homo sapiens calcium responsive transcription factor (CARF), transcript variant 4, mRNA
gi|1890275068|ref|NM_001282911.3|

Nucleotide
Homo sapiens calcium responsive transcription factor (CARF), transcript variant ...
Homo sapiens calcium responsive transcription factor (CARF), transcript variant 14, mRNA
gi|1676439701|ref|NM_001352676.2|

Nucleotide
Rattus norvegicus partner of NOB1 homolog (S. cerevisiae) (Pno1), mRNA
Rattus norvegicus partner of NOB1 homolog (S. cerevisiae) (Pno1), mRNA
gi|40018533|ref|NM_199083.1|

Nucleotide
Homo sapiens LBH domain containing 1 (LBHD1), transcript variant 7, mRNA
Homo sapiens LBH domain containing 1 (LBHD1), transcript variant 7, mRNA
gi|2030184128|ref|NM_001394604.1|

Nucleotide
ART1 [Orcinus orca]
ART1 [Orcinus orca]
Gene ID:101287676

Gene

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
SCV004121346	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 21, 2023)	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

SCV004121346

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 21, 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	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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004121346.1

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

Description

The ATM c.6177dupA variant is predicted to result in a frameshift and premature protein termination (p.Arg2060Thrfs*28). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/654478/). Frameshift variants in ATM are expected to be pathogenic. This variant is interpreted 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: Oct 26, 2024

ClinVar

Relating variation to medicine