VCV001340046.2 - ClinVar

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

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

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

Variation ID: 1340046 Accession: VCV001340046.2

Type and length

copy number loss, 745,048 bp

Location

Cytogenetic: 22q11.21 22: 21059669-21804716 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 13, 2022	Jan 26, 2024	Aug 26, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000022.10:g.(?_21059669)_(21804716_?)del

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
CRKL		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	27	430
AIFM3		-	-	GRCh38 GRCh37	42	446
GGT2		-	-	GRCh38 GRCh37	9	148
HIC2		-	-	GRCh38 GRCh37	52	189
LZTR1		-	-	GRCh38 GRCh37	3176	3687
P2RX6		-	-	GRCh38 GRCh37	37	432
PI4KA		-	-	GRCh38 GRCh37	310	792
RIMBP3B		-	-	GRCh38 GRCh37	25	143
SERPIND1		-	-	GRCh38 GRCh37	-	470
SLC7A4		-	-	GRCh38 GRCh37	69	461

There are 2 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37) and ClinGen Dosage Sensitivity Map.

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Likely pathogenic (1)	criteria provided, single submitter	Aug 26, 2022	RCV001827632.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Aug 26, 2022)	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019) Method: clinical testing	not provided Affected status: unknown Allele origin: unknown	Quest Diagnostics Nichols Institute San Juan Capistrano Accession: SCV002095981.2 First in ClinVar: Feb 13, 2022 Last updated: Jan 26, 2024	Comment: 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 … (more) 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 (less)

Comment:

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

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Feb 04, 2024

ClinVar Genomic variation as it relates to human health

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

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...