NM_000051.4(ATM):c.7942C>T (p.Pro2648Ser) AND Ataxia-telangiectasia syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 17, 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:: RCV001221756.16

Allele description [Variation Report for NM_000051.4(ATM):c.7942C>T (p.Pro2648Ser)]

NM_000051.4(ATM):c.7942C>T (p.Pro2648Ser)

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.7942C>T (p.Pro2648Ser)

HGVS:

NC_000011.10:g.108333900C>T
NG_009830.1:g.116069C>T
NG_054724.1:g.140933G>A
NM_000051.4:c.7942C>TMANE SELECT
NM_001330368.2:c.641-24829G>A
NM_001351110.2:c.*38+1320G>A
NM_001351834.2:c.7942C>T
NP_000042.3:p.Pro2648Ser
NP_000042.3:p.Pro2648Ser
NP_001338763.1:p.Pro2648Ser
LRG_135t1:c.7942C>T
LRG_135:g.116069C>T
LRG_135p1:p.Pro2648Ser
NC_000011.9:g.108204627C>T
NM_000051.3:c.7942C>T

Protein change:

P2648S

Links:

dbSNP: rs878853547

NCBI 1000 Genomes Browser:

rs878853547

Molecular consequence:

NM_001330368.2:c.641-24829G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+1320G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.7942C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.7942C>T - 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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cellular organisms
cellular organisms
De novo sequencing and analysis for JCM strains in GCM 10K project

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BioProject Links for Nucleotide (Select 2682066976) (1)
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Pontixanthobacter gangjinensis JCM 17802 DNA, sequence16, whole genome shotgun s...
Pontixanthobacter gangjinensis JCM 17802 DNA, sequence16, whole genome shotgun sequence
gi|2682066969|dbj|BAABFK010000016.1 |WGS:BAABFK01|sequence16

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001393818	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 17, 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

SCV001393818

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 17, 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

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, SCV001393818.5

#	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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 950115). This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 2648 of the ATM protein (p.Pro2648Ser).

#	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: Nov 10, 2024

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Relating variation to medicine