NM_000051.4(ATM):c.7088del (p.Lys2363fs) AND Ataxia-telangiectasia syndrome

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

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Sep 8, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000223734.18

Allele description

NM_000051.4(ATM):c.7088del (p.Lys2363fs)

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.7088del (p.Lys2363fs)

HGVS:

NC_000011.10:g.108327757del
NG_009830.1:g.109926del
NG_054724.1:g.147079del
NM_000051.4:c.7088delMANE SELECT
NM_001330368.2:c.641-18683del
NM_001351110.2:c.*38+7466del
NM_001351834.2:c.7088del
NP_000042.3:p.Lys2363Argfs
NP_000042.3:p.Lys2363fs
NP_001338763.1:p.Lys2363fs
LRG_135t1:c.7088del
LRG_135:g.109926del
NC_000011.10:g.108327757delA
NC_000011.9:g.108198481del
NC_000011.9:g.108198484del
NM_000051.3:c.7088del
NM_000051.3:c.7088delA

Protein change:

K2363fs

Links:

dbSNP: rs876658512

NCBI 1000 Genomes Browser:

rs876658512

Molecular consequence:

NM_000051.4:c.7088del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001351834.2:c.7088del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330368.2:c.641-18683del - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+7466del - 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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Taxonomy Links for GEO Profiles (Select 127948633) (1)
Taxonomy
BioProject Links for Protein (Select 2124314213) (1)
BioProject
Homo sapiens signaling receptor and transporter of retinol STRA6 (STRA6), transc...
Homo sapiens signaling receptor and transporter of retinol STRA6 (STRA6), transcript variant 2, mRNA
gi|1519311603|ref|NM_022369.4|

Nucleotide
Batrachochytrium salamandrivorans strain AMFP15/1 contig_1029, whole genome shot...
Batrachochytrium salamandrivorans strain AMFP15/1 contig_1029, whole genome shotgun sequence
gi|2124313993|gb|JAFDOV010000021.1| WGS:JAFDOV01|contig_1029

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267593	Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology	no assertion criteria provided	Pathogenic	somatic	research
SCV001585435	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 8, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23807571, 25614872, 29163336, 28492532
SCV001810279	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 22, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267593

Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology

no assertion criteria provided

Pathogenic

somatic

research

SCV001585435

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 8, 2023)

germline

clinical testing

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

SCV001810279

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 22, 2021)

germline

clinical testing

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

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
not provided	somatic	no	4	1	not provided	not provided	not provided	research
not provided	somatic	yes	2	1	not provided	not provided	not provided	research
not provided	germline	no	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 (5)

Details of each submission

From Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, SCV000267593.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	research	not provided
2	not provided	4	not provided	not provided	research	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	somatic	yes	not provided	not provided	not provided		2	not provided	1	not provided
2	somatic	no	not provided	not provided	not provided		4	not provided	1	not provided

From Invitae, SCV001585435.4

#	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 creates a premature translational stop signal (p.Lys2363Argfs*3) in the ATM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with ataxia telangiectasia (PMID: 29163336). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 230341). 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 Genome-Nilou Lab, SCV001810279.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 16, 2024

ClinVar

Relating variation to medicine