NM_000051.4(ATM):c.1921GAA[1] (p.Glu642del) AND Ataxia-telangiectasia syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 29, 2022
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:: RCV000529776.10

Allele description [Variation Report for NM_000051.4(ATM):c.1921GAA[1] (p.Glu642del)]

NM_000051.4(ATM):c.1921GAA[1] (p.Glu642del)

Gene:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.1921GAA[1] (p.Glu642del)

Other names:

NP_000042.3:p.Glu642del; p.Glu642del

HGVS:

NC_000011.10:g.108253836GAA[1]
NG_009830.1:g.36005GAA[1]
NM_000051.4:c.1921GAA[1]MANE SELECT
NM_001351834.2:c.1921GAA[1]
NP_000042.3:p.Glu642del
NP_001338763.1:p.Glu642del
LRG_135t1:c.1924_1926del
LRG_135:g.36005GAA[1]
NC_000011.9:g.108124561_108124563del
NC_000011.9:g.108124563GAA[1]
NM_000051.3:c.1924_1926del
NM_000051.3:c.1924_1926delGAA
NM_000051.4:c.1924_1926delMANE SELECT

Protein change:

E642del

Links:

dbSNP: rs876659575

NCBI 1000 Genomes Browser:

rs876659575

Molecular consequence:

NM_000051.4:c.1921GAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001351834.2:c.1921GAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000622294	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 29, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002083905	Natera, Inc.	no assertion criteria provided	Uncertain significance (Aug 18, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000622294

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 29, 2022)

germline

clinical testing

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

SCV002083905

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Aug 18, 2021)

germline

clinical testing

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000622294.7

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

Description

This variant, c.1924_1926del, results in the deletion of 1 amino acid(s) of the ATM protein (p.Glu642del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant has been observed to be homozygous or hemizygous in an individual who did not have the expected clinical features for that genetic result (Invitae). ClinVar contains an entry for this variant (Variation ID: 232133). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 Natera, Inc., SCV002083905.1

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

Last Updated: Sep 29, 2024

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