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NC_000011.9:g.(?_94153285)_(111965700_?)del AND Ataxia-telangiectasia syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 16, 2020
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:
RCV001389105.2

Allele description [Variation Report for NC_000011.9:g.(?_94153285)_(111965700_?)del]

NC_000011.9:g.(?_94153285)_(111965700_?)del

Genes:
  • ALG9:ALG9 alpha-1,2-mannosyltransferase [Gene - OMIM - HGNC]
  • ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
  • BTG4:BTG anti-proliferation factor 4 [Gene - OMIM - HGNC]
  • CWC15:CWC15 spliceosome associated protein homolog [Gene - HGNC]
  • CWF19L2:CWF19 like cell cycle control factor 2 [Gene - HGNC]
  • DDX10:DEAD-box helicase 10 [Gene - OMIM - HGNC]
  • DIXDC1:DIX domain containing 1 [Gene - OMIM - HGNC]
  • DDI1:DNA damage inducible 1 homolog 1 [Gene - HGNC]
  • ELMOD1:ELMO domain containing 1 [Gene - OMIM - HGNC]
  • HOATZ:HOATZ cilia and flagella associated protein [Gene - HGNC]
  • JRKL:JRK like [Gene - OMIM - HGNC]
  • MIR34BHG:MIR34B and MIR34C host gene [Gene - HGNC]
  • MRE11:MRE11 homolog, double strand break repair nuclease [Gene - OMIM - HGNC]
  • MSANTD4:Myb/SANT DNA binding domain containing 4 with coiled-coils [Gene - HGNC]
  • NKAPD1:NKAP domain containing 1 [Gene - HGNC]
  • PIH1D2:PIH1 domain containing 2 [Gene - HGNC]
  • POU2AF1:POU class 2 homeobox associating factor 1 [Gene - OMIM - HGNC]
  • POU2AF2:POU class 2 homeobox associating factor 2 [Gene - HGNC]
  • POU2AF3:POU class 2 homeobox associating factor 3 [Gene - OMIM - HGNC]
  • RAB39A:RAB39A, member RAS oncogene family [Gene - OMIM - HGNC]
  • ARHGAP20:Rho GTPase activating protein 20 [Gene - OMIM - HGNC]
  • ARHGAP42:Rho GTPase activating protein 42 [Gene - OMIM - HGNC]
  • YAP1:Yes1 associated transcriptional regulator [Gene - OMIM - HGNC]
  • ACAT1:acetyl-CoA acetyltransferase 1 [Gene - OMIM - HGNC]
  • ALKBH8:alkB homolog 8, tRNA methyltransferase [Gene - OMIM - HGNC]
  • AASDHPPT:aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase [Gene - OMIM - HGNC]
  • AMOTL1:angiomotin like 1 [Gene - OMIM - HGNC]
  • ANGPTL5:angiopoietin like 5 [Gene - OMIM - HGNC]
  • ANKRD49:ankyrin repeat domain 49 [Gene - OMIM - HGNC]
  • BIRC2:baculoviral IAP repeat containing 2 [Gene - OMIM - HGNC]
  • BIRC3:baculoviral IAP repeat containing 3 [Gene - OMIM - HGNC]
  • CASP12:caspase 12 (gene/pseudogene) [Gene - OMIM - HGNC]
  • CASP1:caspase 1 [Gene - OMIM - HGNC]
  • CASP4:caspase 4 [Gene - OMIM - HGNC]
  • CASP5:caspase 5 [Gene - OMIM - HGNC]
  • CARD16:caspase recruitment domain family member 16 [Gene - OMIM - HGNC]
  • CARD17:caspase recruitment domain family member 17 [Gene - OMIM - HGNC]
  • CARD18:caspase recruitment domain family member 18 [Gene - OMIM - HGNC]
  • CEP126:centrosomal protein 126 [Gene - OMIM - HGNC]
  • CEP57:centrosomal protein 57 [Gene - OMIM - HGNC]
  • C11orf52:chromosome 11 open reading frame 52 [Gene - HGNC]
  • C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]
  • C11orf87:chromosome 11 open reading frame 87 [Gene - HGNC]
  • CFAP300:cilia and flagella associated protein 300 [Gene - OMIM - HGNC]
  • CFAP68:cilia and flagella associated protein 68 [Gene - HGNC]
  • CCDC82:coiled-coil domain containing 82 [Gene - OMIM - HGNC]
  • CNTN5:contactin 5 [Gene - OMIM - HGNC]
  • CRYAB:crystallin alpha B [Gene - OMIM - HGNC]
  • CUL5:cullin 5 [Gene - OMIM - HGNC]
  • DCUN1D5:defective in cullin neddylation 1 domain containing 5 [Gene - OMIM - HGNC]
  • DLAT:dihydrolipoamide S-acetyltransferase [Gene - OMIM - HGNC]
  • DYNC2H1:dynein cytoplasmic 2 heavy chain 1 [Gene - OMIM - HGNC]
  • ENDOD1:endonuclease domain containing 1 [Gene - OMIM - HGNC]
  • EXPH5:exophilin 5 [Gene - OMIM - HGNC]
  • FAM76B:family with sequence similarity 76 member B [Gene - HGNC]
  • FDX1:ferredoxin 1 [Gene - OMIM - HGNC]
  • FDXACB1:ferredoxin-fold anticodon binding domain containing 1 [Gene - HGNC]
  • FUT4:fucosyltransferase 4 [Gene - OMIM - HGNC]
  • GRIA4:glutamate ionotropic receptor AMPA type subunit 4 [Gene - OMIM - HGNC]
  • GUCY1A2:guanylate cyclase 1 soluble subunit alpha 2 [Gene - OMIM - HGNC]
  • HSPB2:heat shock protein family B (small) member 2 [Gene - OMIM - HGNC]
  • KBTBD3:kelch repeat and BTB domain containing 3 [Gene - HGNC]
  • LAYN:layilin [Gene - OMIM - HGNC]
  • KDM4D:lysine demethylase 4D [Gene - OMIM - HGNC]
  • KDM4E:lysine demethylase 4E [Gene - OMIM - HGNC]
  • MAML2:mastermind like transcriptional coactivator 2 [Gene - OMIM - HGNC]
  • LOC100128088:matrix metallopeptidase 1-like [Gene]
  • MMP10:matrix metallopeptidase 10 [Gene - OMIM - HGNC]
  • MMP12:matrix metallopeptidase 12 [Gene - OMIM - HGNC]
  • MMP13:matrix metallopeptidase 13 [Gene - OMIM - HGNC]
  • MMP1:matrix metallopeptidase 1 [Gene - OMIM - HGNC]
  • MMP20:matrix metallopeptidase 20 [Gene - OMIM - HGNC]
  • MMP27:matrix metallopeptidase 27 [Gene - OMIM - HGNC]
  • MMP3:matrix metallopeptidase 3 [Gene - OMIM - HGNC]
  • MMP7:matrix metallopeptidase 7 [Gene - OMIM - HGNC]
  • MMP8:matrix metallopeptidase 8 [Gene - OMIM - HGNC]
  • MIR34B:microRNA 34b [Gene - OMIM - HGNC]
  • MIR34C:microRNA 34c [Gene - OMIM - HGNC]
  • MTMR2:myotubularin related protein 2 [Gene - OMIM - HGNC]
  • NPAT:nuclear protein, coactivator of histone transcription [Gene - OMIM - HGNC]
  • PIWIL4:piwi like RNA-mediated gene silencing 4 [Gene - OMIM - HGNC]
  • PDGFD:platelet derived growth factor D [Gene - OMIM - HGNC]
  • PGR:progesterone receptor [Gene - OMIM - HGNC]
  • POGLUT3:protein O-glucosyltransferase 3 [Gene - OMIM - HGNC]
  • PPP2R1B:protein phosphatase 2 scaffold subunit Abeta [Gene - OMIM - HGNC]
  • RDX:radixin [Gene - OMIM - HGNC]
  • SIK2:salt inducible kinase 2 [Gene - OMIM - HGNC]
  • SLN:sarcolipin [Gene - OMIM - HGNC]
  • SRSF8:serine and arginine rich splicing factor 8 [Gene - OMIM - HGNC]
  • SESN3:sestrin 3 [Gene - OMIM - HGNC]
  • SLC35F2:solute carrier family 35 member F2 [Gene - HGNC]
  • SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]
  • TRPC6:transient receptor potential cation channel subfamily C member 6 [Gene - OMIM - HGNC]
  • TIMM8B:translocase of inner mitochondrial membrane 8 homolog B [Gene - OMIM - HGNC]
  • TMEM123:transmembrane protein 123 [Gene - OMIM - HGNC]
  • TMEM133:transmembrane protein 133 [Gene - HGNC]
  • ZC3H12C:zinc finger CCCH-type containing 12C [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q21-23.1
Genomic location:
Chr11: 94153285 - 111965700 (on Assembly GRCh37)
Preferred name:
NC_000011.9:g.(?_94153285)_(111965700_?)del
HGVS:
NC_000011.9:g.(?_94153285)_(111965700_?)del

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001590313Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 16, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV001590313.2

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the ATM gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with ATM-related conditions. 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: Mar 26, 2023