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NC_000022.10:g.(?_17565982)_(20052185_?)del AND Vasculitis due to ADA2 deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 17, 2022
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:
RCV003107327.4

Allele description [Variation Report for NC_000022.10:g.(?_17565982)_(20052185_?)del]

NC_000022.10:g.(?_17565982)_(20052185_?)del

Genes:
  • ARVCF:ARVCF delta catenin family member [Gene - OMIM - HGNC]
  • ATP6V1E1:ATPase H+ transporting V1 subunit E1 [Gene - OMIM - HGNC]
  • BCL2L13:BCL2 like 13 [Gene - OMIM - HGNC]
  • BID:BH3 interacting domain death agonist [Gene - OMIM - HGNC]
  • CECR2:CECR2 histone acetyl-lysine reader [Gene - OMIM - HGNC]
  • DGCR2:DiGeorge syndrome critical region gene 2 [Gene - OMIM - HGNC]
  • DGCR6:DiGeorge syndrome critical region gene 6 [Gene - OMIM - HGNC]
  • GNB1L:G protein subunit beta 1 like [Gene - OMIM - HGNC]
  • TBX1:T-box transcription factor 1 [Gene - OMIM - HGNC]
  • ADA2:adenosine deaminase 2 [Gene - OMIM - HGNC]
  • CECR3:cat eye syndrome chromosome region, candidate 3 [Gene - HGNC]
  • COMT:catechol-O-methyltransferase [Gene - OMIM - HGNC]
  • CDC45:cell division cycle 45 [Gene - OMIM - HGNC]
  • C22orf39:chromosome 22 open reading frame 39 [Gene - HGNC]
  • CLTCL1:clathrin heavy chain like 1 [Gene - OMIM - HGNC]
  • CLDN5:claudin 5 [Gene - OMIM - HGNC]
  • ESS2:ess-2 splicing factor homolog [Gene - OMIM - HGNC]
  • GP1BB:glycoprotein Ib platelet subunit beta [Gene - OMIM - HGNC]
  • GSC2:goosecoid homeobox 2 [Gene - OMIM - HGNC]
  • HDHD5:haloacid dehalogenase like hydrolase domain containing 5 [Gene - HGNC]
  • HIRA:histone cell cycle regulator [Gene - OMIM - HGNC]
  • IL17RA:interleukin 17 receptor A [Gene - OMIM - HGNC]
  • MICAL3:microtubule associated monooxygenase, calponin and LIM domain containing 3 [Gene - OMIM - HGNC]
  • MRPL40:mitochondrial ribosomal protein L40 [Gene - OMIM - HGNC]
  • PEX26:peroxisomal biogenesis factor 26 [Gene - OMIM - HGNC]
  • PRODH:proline dehydrogenase 1 [Gene - OMIM - HGNC]
  • RTL10:retrotransposon Gag like 10 [Gene - OMIM - HGNC]
  • SEPTIN5:septin 5 [Gene - OMIM - HGNC]
  • SLC25A18:solute carrier family 25 member 18 [Gene - OMIM - HGNC]
  • SLC25A1:solute carrier family 25 member 1 [Gene - OMIM - HGNC]
  • TSSK2:testis specific serine kinase 2 [Gene - OMIM - HGNC]
  • TXNRD2:thioredoxin reductase 2 [Gene - OMIM - HGNC]
  • TMEM121B:transmembrane protein 121B [Gene - HGNC]
  • TANGO2:transport and golgi organization 2 homolog [Gene - OMIM - HGNC]
  • TUBA8:tubulin alpha 8 [Gene - OMIM - HGNC]
  • UFD1:ubiquitin recognition factor in ER associated degradation 1 [Gene - OMIM - HGNC]
  • USP18:ubiquitin specific peptidase 18 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q11.1-11.21
Genomic location:
Chr22: 17565982 - 20052185 (on Assembly GRCh37)
Preferred name:
NC_000022.10:g.(?_17565982)_(20052185_?)del
HGVS:
NC_000022.10:g.(?_17565982)_(20052185_?)del

Condition(s)

Name:
Vasculitis due to ADA2 deficiency (VAIHS)
Synonyms:
Polyarteritis nodosa, childhoood-onset; VASCULITIS, AUTOINFLAMMATION, IMMUNODEFICIENCY, AND HEMATOLOGIC DEFECTS SYNDROME
Identifiers:
MONDO: MONDO:0014306; MedGen: C3887654; Orphanet: 404553; OMIM: 615688

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003793505Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 17, 2022) 		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

Early-onset stroke and vasculopathy associated with mutations in ADA2.

Zhou Q, Yang D, Ombrello AK, Zavialov AV, Toro C, Zavialov AV, Stone DL, Chae JJ, Rosenzweig SD, Bishop K, Barron KS, Kuehn HS, Hoffmann P, Negro A, Tsai WL, Cowen EW, Pei W, Milner JD, Silvin C, Heller T, Chin DT, Patronas NJ, et al.

N Engl J Med. 2014 Mar 6;370(10):911-20. doi: 10.1056/NEJMoa1307361. Epub 2014 Feb 19.

PubMed [citation]
PMID:
24552284
PMCID:
PMC4193683

Mutant adenosine deaminase 2 in a polyarteritis nodosa vasculopathy.

Navon Elkan P, Pierce SB, Segel R, Walsh T, Barash J, Padeh S, Zlotogorski A, Berkun Y, Press JJ, Mukamel M, Voth I, Hashkes PJ, Harel L, Hoffer V, Ling E, Yalcinkaya F, Kasapcopur O, Lee MK, Klevit RE, Renbaum P, Weinberg-Shukron A, Sener EF, et al.

N Engl J Med. 2014 Mar 6;370(10):921-31. doi: 10.1056/NEJMoa1307362. Epub 2014 Feb 19.

PubMed [citation]
PMID:
24552285
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003793505.2

#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 ADA2 gene has been identified. Loss-of-function variants in ADA2 are known to be pathogenic (PMID: 24552284, 24552285). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with ADA2-related conditions. 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: Sep 29, 2024