NM_000051.4(ATM):c.6067G>A (p.Gly2023Arg) AND Ataxia-telangiectasia syndrome

Germline classification:: Conflicting interpretations of pathogenicity (6 submissions)
Last evaluated:: Feb 1, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000122864.38

Allele description [Variation Report for NM_000051.4(ATM):c.6067G>A (p.Gly2023Arg)]

NM_000051.4(ATM):c.6067G>A (p.Gly2023Arg)

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.6067G>A (p.Gly2023Arg)

Other names:

p.G2023R:GGA>AGA; NP_000042.3:p.Gly2023Arg

HGVS:

NC_000011.10:g.108315883G>A
NG_009830.1:g.98052G>A
NG_054724.1:g.158950C>T
NM_000051.4:c.6067G>AMANE SELECT
NM_001330368.2:c.641-6812C>T
NM_001351110.2:c.*39-6812C>T
NM_001351834.2:c.6067G>A
NP_000042.3:p.Gly2023Arg
NP_000042.3:p.Gly2023Arg
NP_001338763.1:p.Gly2023Arg
LRG_135t1:c.6067G>A
LRG_135:g.98052G>A
LRG_135p1:p.Gly2023Arg
NC_000011.9:g.108186610G>A
NM_000051.3:c.6067G>A
Q13315:p.Gly2023Arg
p.G2023R

Protein change:

G2023R

Links:

UniProtKB: Q13315#VAR_077238; dbSNP: rs11212587

NCBI 1000 Genomes Browser:

rs11212587

Molecular consequence:

NM_001330368.2:c.641-6812C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-6812C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.6067G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.6067G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000166122	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000838565	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Benign (Aug 22, 2023)	germline	clinical testing	Citation Link,
SCV001263992	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 26094658, 25625042, 23091097, 19404735, 11505391, 12810666, 17393301 Citation Link,
SCV001452119	Natera, Inc.	no assertion criteria provided	Likely benign (Apr 18, 2020)	germline	clinical testing
SCV001781325	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 14, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003931264	GenomeConnect - Brain Gene Registry	no classification provided	not provided	unknown	phenotyping only

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	1	not provided	not provided	1	not provided	phenotyping only
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
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

Detection of novel germline mutations for breast cancer in non-BRCA1/2 families.

Aloraifi F, McDevitt T, Martiniano R, McGreevy J, McLaughlin R, Egan CM, Cody N, Meany M, Kenny E, Green AJ, Bradley DG, Geraghty JG, Bracken AP.

FEBS J. 2015 Sep;282(17):3424-37. doi: 10.1111/febs.13352. Epub 2015 Jul 14.

PubMed [citation]

PMID:: 26094658

See all PubMed Citations (9)

Details of each submission

From Invitae, SCV000166122.14

#	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 Mendelics, SCV000838565.3

#	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

From Illumina Laboratory Services, Illumina, SCV001263992.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown 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., SCV001452119.1

#	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

From Genome-Nilou Lab, SCV001781325.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GenomeConnect - Brain Gene Registry, SCV003931264.1

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

Description

Variant classified as Uncertain significance and reported on 02-03-2017 by Baylor Medical Genetics Laboratories. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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

Last Updated: Aug 18, 2024

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