NM_000051.4(ATM):c.2134T>A (p.Ser712Thr) AND Ataxia-telangiectasia syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 8, 2019
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:: RCV001226941.7

Allele description [Variation Report for NM_000051.4(ATM):c.2134T>A (p.Ser712Thr)]

NM_000051.4(ATM):c.2134T>A (p.Ser712Thr)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.2134T>A (p.Ser712Thr)

HGVS:

NC_000011.10:g.108256224T>A
NG_009830.1:g.38393T>A
NM_000051.4:c.2134T>AMANE SELECT
NM_001351834.2:c.2134T>A
NP_000042.3:p.Ser712Thr
NP_001338763.1:p.Ser712Thr
LRG_135t1:c.2134T>A
LRG_135:g.38393T>A
NC_000011.9:g.108126951T>A
NM_000051.3:c.2134T>A

Protein change:

S712T

Links:

dbSNP: rs1565394509

NCBI 1000 Genomes Browser:

rs1565394509

Molecular consequence:

NM_000051.4:c.2134T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.2134T>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

Recent activity

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LOC18585703 [Theobroma cacao]
LOC18585703 [Theobroma cacao]
Gene ID:18585703

Gene
XM_018129523.1 AND (alive[prop]) (1)
Gene
Borreria verticillata (121)
Nucleotide
JGI_CABC8100.rev NIH_XGC_tropFat1 Xenopus tropicalis cDNA clone IMAGE:7804451 3'...
JGI_CABC8100.rev NIH_XGC_tropFat1 Xenopus tropicalis cDNA clone IMAGE:7804451 3', mRNA sequence
gi|71495502|gnl|dbEST|30359271|gb|D 48.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001399273	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 8, 2019)	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

SCV001399273

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 8, 2019)

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

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, SCV001399273.5

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with ATM-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with threonine at codon 712 of the ATM protein (p.Ser712Thr). The serine residue is weakly conserved and there is a small physicochemical difference between serine and threonine.

#	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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