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GRCh37/hg19 22q11.21(chr22:21059669-21804716)x1 AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 26, 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:
RCV001827632.2

Allele description [Variation Report for GRCh37/hg19 22q11.21(chr22:21059669-21804716)x1]

GRCh37/hg19 22q11.21(chr22:21059669-21804716)x1

Genes:
  • CRKL:CRK like proto-oncogene, adaptor protein [Gene - OMIM - HGNC]
  • HIC2:HIC ZBTB transcriptional repressor 2 [Gene - OMIM - HGNC]
  • RIMBP3B:RIMS binding protein 3B [Gene - OMIM - HGNC]
  • THAP7:THAP domain containing 7 [Gene - OMIM - HGNC]
  • AIFM3:apoptosis inducing factor mitochondria associated 3 [Gene - OMIM - HGNC]
  • GGT2:gamma-glutamyltransferase 2 [Gene - OMIM - HGNC]
  • LZTR1:leucine zipper like post translational regulator 1 [Gene - OMIM - HGNC]
  • PI4KA:phosphatidylinositol 4-kinase alpha [Gene - OMIM - HGNC]
  • P2RX6:purinergic receptor P2X 6 [Gene - OMIM - HGNC]
  • SERPIND1:serpin family D member 1 [Gene - OMIM - HGNC]
  • SLC7A4:solute carrier family 7 member 4 [Gene - OMIM - HGNC]
  • SNAP29:synaptosome associated protein 29 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
22q11.21
Genomic location:
Chr22: 21059669 - 21804716 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 22q11.21(chr22:21059669-21804716)x1
HGVS:
NC_000022.10:g.(?_21059669)_(21804716_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002095981Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)		Likely pathogenic
(Aug 26, 2022) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]
PMID:
31690835
PMCID:
PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002095981.2

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

Description

This copy number loss involves multiple coding genes and overlaps the 22q11.2 central deletion (LCR C-D) syndromic region. It has been proposed that haploinsufficiency of CRKL contributes to the deletion 22q11.2 phenotype (Racedo 2015). While there are multiple copy number losses which cover the majority of this region in the general populations of the Database of Genomic Variants, a single study demonstrates enrichment of the LCR C-D deletion in patients with congenital kidney and urinary tract anomalies compared to controls (Lopez-Rivera 2017). Thus, this copy number loss is interpreted as likely pathogenic with reduced penetrance and variable expressivity (Burnside 2015). References: Burnside RD, Cytogenet Genome Res. 2015;146(2):89-99. PMID: 26278718 Lopez-Rivera et al. N Engl J Med. 2017;376(8):742-754. PMID: 28121514 Racedo et al. Am J Hum Genet. 2015;96(2):235-44. PMID: 25658046

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 4, 2024