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NM_000051.4(ATM):c.7793G>A (p.Arg2598Gln) AND Ataxia-telangiectasia syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 27, 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:
RCV000463904.18

Allele description [Variation Report for NM_000051.4(ATM):c.7793G>A (p.Arg2598Gln)]

NM_000051.4(ATM):c.7793G>A (p.Arg2598Gln)

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.7793G>A (p.Arg2598Gln)
HGVS:
  • NC_000011.10:g.108332766G>A
  • NG_009830.1:g.114935G>A
  • NG_054724.1:g.142067C>T
  • NM_000051.4:c.7793G>AMANE SELECT
  • NM_001330368.2:c.641-23695C>T
  • NM_001351110.2:c.*38+2454C>T
  • NM_001351834.2:c.7793G>A
  • NP_000042.3:p.Arg2598Gln
  • NP_000042.3:p.Arg2598Gln
  • NP_001338763.1:p.Arg2598Gln
  • LRG_135t1:c.7793G>A
  • LRG_135:g.114935G>A
  • LRG_135p1:p.Arg2598Gln
  • NC_000011.9:g.108203493G>A
  • NM_000051.3:c.7793G>A
Protein change:
R2598Q
Links:
dbSNP: rs140263969
NCBI 1000 Genomes Browser:
rs140263969
Molecular consequence:
  • NM_001330368.2:c.641-23695C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*38+2454C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.7793G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.7793G>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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000546708Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 27, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Detection of inherited mutations for hereditary cancer using target enrichment and next generation sequencing.

Guan Y, Hu H, Peng Y, Gong Y, Yi Y, Shao L, Liu T, Li G, Wang R, Dai P, Bignon YJ, Xiao Z, Yang L, Mu F, Xiao L, Xie Z, Yan W, Xu N, Zhou D, Yi X.

Fam Cancer. 2015 Mar;14(1):9-18. doi: 10.1007/s10689-014-9749-9.

PubMed [citation]
PMID:
25151137

Unexpected cancer-predisposition gene variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome patients without underlying germline PTEN mutations.

Yehia L, Ni Y, Sesock K, Niazi F, Fletcher B, Chen HJL, LaFramboise T, Eng C.

PLoS Genet. 2018 Apr;14(4):e1007352. doi: 10.1371/journal.pgen.1007352.

PubMed [citation]
PMID:
29684080
PMCID:
PMC5933810
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000546708.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 2598 of the ATM protein (p.Arg2598Gln). This variant is present in population databases (rs140263969, gnomAD 0.008%). This missense change has been observed in individual(s) with clinical features of ATM-related conditions (PMID: 25151137, 29684080). ClinVar contains an entry for this variant (Variation ID: 229826). 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. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024