NM_000051.4(ATM):c.6164_6165del (p.Ile2055fs) AND Ataxia-telangiectasia syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 18, 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:: RCV001053229.13

Allele description [Variation Report for NM_000051.4(ATM):c.6164_6165del (p.Ile2055fs)]

NM_000051.4(ATM):c.6164_6165del (p.Ile2055fs)

Genes:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.6164_6165del (p.Ile2055fs)

HGVS:

NC_000011.10:g.108316079_108316080del
NG_009830.1:g.98248_98249del
NG_054724.1:g.158753_158754del
NM_000051.4:c.6164_6165delMANE SELECT
NM_001330368.2:c.641-7009_641-7008del
NM_001351110.2:c.*39-7009_*39-7008del
NM_001351834.2:c.6164_6165del
NP_000042.3:p.Ile2055Thrfs
NP_000042.3:p.Ile2055fs
NP_001338763.1:p.Ile2055fs
LRG_135t1:c.6164_6165del
LRG_135:g.98248_98249del
NC_000011.9:g.108186806_108186807del
NM_000051.3:c.6164_6165del
NM_000051.3:c.6164_6165delTC

Protein change:

I2055fs

Links:

dbSNP: rs2084621452

NCBI 1000 Genomes Browser:

rs2084621452

Molecular consequence:

NM_000051.4:c.6164_6165del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001351834.2:c.6164_6165del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330368.2:c.641-7009_641-7008del - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-7009_*39-7008del - intron variant - [Sequence Ontology: SO:0001627]

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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leucine-rich repeat-containing protein 45 [Homo sapiens]
leucine-rich repeat-containing protein 45 [Homo sapiens]
gi|21450705|ref|NP_659436.1|

Protein
LOC130067958 [Homo sapiens]
LOC130067958 [Homo sapiens]
Gene ID:130067958

Gene
LOC130067973 [Homo sapiens]
LOC130067973 [Homo sapiens]
Gene ID:130067973

Gene
atp5po.S ATP synthase peripheral stalk subunit OSCP S homeolog [Xenopus laevis]
atp5po.S ATP synthase peripheral stalk subunit OSCP S homeolog [Xenopus laevis]
Gene ID:446923

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001217479	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 18, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23807571, 25614872, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001217479

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 18, 2019)

germline

clinical testing

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

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

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

Ten new ATM alterations in Polish patients with ataxia-telangiectasia.

Podralska MJ, Stembalska A, Ślęzak R, Lewandowicz-Uszyńska A, Pietrucha B, Kołtan S, Wigowska-Sowińska J, Pilch J, Mosor M, Ziółkowska-Suchanek I, Dzikiewicz-Krawczyk A, Słomski R.

Mol Genet Genomic Med. 2014 Nov;2(6):504-11. doi: 10.1002/mgg3.98. Epub 2014 Jul 30.

PubMed [citation]

PMID:: 25614872
PMCID:: PMC4303220

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001217479.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). 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 creates a premature translational stop signal (p.Ile2055Thrfs*32) in the ATM gene. It is expected to result in an absent or disrupted protein product.

#	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: Oct 26, 2024

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