NM_000051.4(ATM):c.6096-9_6096-5del AND Ataxia-telangiectasia syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Sep 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:: RCV000793448.17

Allele description

NM_000051.4(ATM):c.6096-9_6096-5del

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.6096-9_6096-5del

HGVS:

NC_000011.10:g.108316002_108316006del
NG_009830.1:g.98171_98175del
NG_054724.1:g.158831_158835del
NM_000051.4:c.6096-9_6096-5delMANE SELECT
NM_001330368.2:c.641-6931_641-6927del
NM_001351110.2:c.*39-6931_*39-6927del
NM_001351834.2:c.6096-9_6096-5del
LRG_135t1:c.6096-9_6096-5del
LRG_135:g.98171_98175del
NC_000011.9:g.108186725_108186729del
NC_000011.9:g.108186729_108186733del
NM_000051.3:c.6096-9_6096-5del
NM_000051.3:c.6096-9_6096-5del5
NM_000051.3:c.6096-9_6096-5delTTCTT

Links:

dbSNP: rs879254095

NCBI 1000 Genomes Browser:

rs879254095

Molecular consequence:

NM_000051.4:c.6096-9_6096-5del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330368.2:c.641-6931_641-6927del - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-6931_*39-6927del - intron variant - [Sequence Ontology: SO:0001627]
NM_001351834.2:c.6096-9_6096-5del - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000932800	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 27, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 9887333, 988733, 18497957, 28492532
SCV002078042	Natera, Inc.	no assertion criteria provided	Uncertain significance (Jul 13, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000932800

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 27, 2023)

germline

clinical testing

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

SCV002078042

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Jul 13, 2020)

germline

clinical testing

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

Characterization of ATM gene mutations in 66 ataxia telangiectasia families.

Sandoval N, Platzer M, Rosenthal A, Dörk T, Bendix R, Skawran B, Stuhrmann M, Wegner RD, Sperling K, Banin S, Shiloh Y, Baumer A, Bernthaler U, Sennefelder H, Brohm M, Weber BH, Schindler D.

Hum Mol Genet. 1999 Jan;8(1):69-79.

PubMed [citation]

PMID:: 9887333

[Vascular permeability in experimental immunologic retinal vasculitis (author's transl)].

Inoue Y, Nomura T, Kodama Y.

Nippon Ganka Gakkai Zasshi. 1976 Aug 10;80(8):658-66. Japanese. No abstract available.

PubMed [citation]

PMID:: 988733

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000932800.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change falls in intron 41 of the ATM gene. It does not directly change the encoded amino acid sequence of the ATM protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has been observed in individual(s) with ataxia-telangiectasia and/or breast cancer (PMID: 9887333, 18497957). This variant is also known as c.6096-9delTTCTT. ClinVar contains an entry for this variant (Variation ID: 246092). Studies have shown that this variant results in skipping of exon 42 (also known as exon 44) and introduces a premature termination codon (PMID: 988733, 18497957; Initae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

#	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

From Natera, Inc., SCV002078042.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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: Sep 16, 2024

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