NM_000051.4(ATM):c.8151G>A (p.Lys2717=) AND Ataxia-telangiectasia syndrome

Clinical significance:Uncertain significance (Last evaluated: Oct 20, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001207545.1

Allele description [Variation Report for NM_000051.4(ATM):c.8151G>A (p.Lys2717=)]

NM_000051.4(ATM):c.8151G>A (p.Lys2717=)

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.8151G>A (p.Lys2717=)
HGVS:
  • NC_000011.10:g.108335109G>A
  • NG_009830.1:g.117278G>A
  • NG_054724.1:g.139724C>T
  • NM_000051.4:c.8151G>AMANE SELECT
  • NM_001330368.2:c.641-26038C>T
  • NM_001351110.2:c.*38+111C>T
  • NM_001351834.2:c.8151G>A
  • NP_000042.3:p.Lys2717=
  • NP_001338763.1:p.Lys2717=
  • LRG_135t1:c.8151G>A
  • LRG_135:g.117278G>A
  • NC_000011.9:g.108205836G>A
  • NM_000051.3:c.8151G>A
Links:
dbSNP: rs1591192550
NCBI 1000 Genomes Browser:
rs1591192550
Molecular consequence:
  • NM_001330368.2:c.641-26038C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*38+111C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.8151G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351834.2:c.8151G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001378905Invitaecriteria provided, single submitter
Uncertain significance
(Oct 20, 2019)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001378905.2

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

Description

This sequence change affects codon 2717 of the ATM mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the ATM protein. This variant also falls at the last nucleotide of exon 55 of the ATM coding sequence, which is part of the consensus splice site for this exon. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with ATM-related conditions. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. 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: Mar 7, 2021

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