NM_000051.4(ATM):c.1753_1756del (p.Leu585fs) AND Ataxia-telangiectasia syndrome

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Jan 14, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000669542.3

Allele description [Variation Report for NM_000051.4(ATM):c.1753_1756del (p.Leu585fs)]

NM_000051.4(ATM):c.1753_1756del (p.Leu585fs)

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.1753_1756del (p.Leu585fs)
HGVS:
  • NC_000011.10:g.108251982_108251985del
  • NG_009830.1:g.34151_34154del
  • NM_000051.4:c.1753_1756delMANE SELECT
  • NM_001351834.2:c.1753_1756del
  • NP_000042.3:p.Leu585fs
  • NP_000042.3:p.Leu585fs
  • NP_001338763.1:p.Leu585fs
  • LRG_135t1:c.1753_1756del
  • LRG_135:g.34151_34154del
  • LRG_135p1:p.Leu585fs
  • NC_000011.9:g.108122707_108122710del
  • NC_000011.9:g.108122709_108122712del
  • NM_000051.3:c.1753_1756del
  • NM_000051.3:c.1753_1756delTTAG
Protein change:
L585fs
Links:
dbSNP: rs1555072008
NCBI 1000 Genomes Browser:
rs1555072008
Molecular consequence:
  • NM_000051.4:c.1753_1756del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351834.2:c.1753_1756del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000794303Counsylcriteria provided, single submitter
Likely pathogenic
(Sep 22, 2017)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV001234031Invitaecriteria provided, single submitter
Pathogenic
(Jan 14, 2019)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Mutations at the ataxia-telangiectasia locus and clinical phenotypes of A-T patients.

Li A, Swift M.

Am J Med Genet. 2000 May 29;92(3):170-7.

PubMed [citation]
PMID:
10817650

Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients.

Huang Y, Yang L, Wang J, Yang F, Xiao Y, Xia R, Yuan X, Yan M.

Neuromolecular Med. 2013 Sep;15(3):536-40. doi: 10.1007/s12017-013-8240-3. Epub 2013 Jun 27. Erratum in: Neuromolecular Med. 2014 Mar;16(1):216.

PubMed [citation]
PMID:
23807571
PMCID:
PMC3732755
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000794303.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001234031.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Leu585Argfs*4) in the ATM gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with ataxia-telangiectasia (PMID: 10817650). This variant is also known as 1753del4 in the literature. ClinVar contains an entry for this variant (Variation ID: 553995). Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Dec 4, 2021

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