GRCh38/hg38 22q11.21(chr22:18718488-20324240)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 22, 2010
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000136577.5

Allele description [Variation Report for GRCh38/hg38 22q11.21(chr22:18718488-20324240)x1]

GRCh38/hg38 22q11.21(chr22:18718488-20324240)x1

Genes:

ARVCF:ARVCF delta catenin family member [Gene - OMIM - HGNC]
LOC130066953:ATAC-STARR-seq lymphoblastoid active region 18658 [Gene]
LOC130066957:ATAC-STARR-seq lymphoblastoid active region 18660 [Gene]
LOC130066959:ATAC-STARR-seq lymphoblastoid active region 18663 [Gene]
LOC130066963:ATAC-STARR-seq lymphoblastoid active region 18664 [Gene]
LOC130066964:ATAC-STARR-seq lymphoblastoid active region 18665 [Gene]
LOC130066968:ATAC-STARR-seq lymphoblastoid active region 18666 [Gene]
LOC130066969:ATAC-STARR-seq lymphoblastoid active region 18667 [Gene]
LOC130066970:ATAC-STARR-seq lymphoblastoid active region 18668 [Gene]
LOC130066971:ATAC-STARR-seq lymphoblastoid active region 18669 [Gene]
LOC130066973:ATAC-STARR-seq lymphoblastoid active region 18670 [Gene]
LOC130066977:ATAC-STARR-seq lymphoblastoid active region 18671 [Gene]
LOC130066982:ATAC-STARR-seq lymphoblastoid active region 18672 [Gene]
LOC130066984:ATAC-STARR-seq lymphoblastoid active region 18673 [Gene]
LOC130066949:ATAC-STARR-seq lymphoblastoid silent region 13451 [Gene]
LOC130066950:ATAC-STARR-seq lymphoblastoid silent region 13452 [Gene]
LOC130066951:ATAC-STARR-seq lymphoblastoid silent region 13454 [Gene]
LOC130066952:ATAC-STARR-seq lymphoblastoid silent region 13457 [Gene]
LOC130066954:ATAC-STARR-seq lymphoblastoid silent region 13459 [Gene]
LOC130066955:ATAC-STARR-seq lymphoblastoid silent region 13460 [Gene]
LOC130066956:ATAC-STARR-seq lymphoblastoid silent region 13462 [Gene]
LOC130066958:ATAC-STARR-seq lymphoblastoid silent region 13463 [Gene]
LOC130066960:ATAC-STARR-seq lymphoblastoid silent region 13467 [Gene]
LOC130066961:ATAC-STARR-seq lymphoblastoid silent region 13468 [Gene]
LOC130066962:ATAC-STARR-seq lymphoblastoid silent region 13469 [Gene]
LOC130066965:ATAC-STARR-seq lymphoblastoid silent region 13470 [Gene]
LOC130066966:ATAC-STARR-seq lymphoblastoid silent region 13471 [Gene]
LOC130066967:ATAC-STARR-seq lymphoblastoid silent region 13472 [Gene]
LOC130066972:ATAC-STARR-seq lymphoblastoid silent region 13473 [Gene]
LOC130066974:ATAC-STARR-seq lymphoblastoid silent region 13474 [Gene]
LOC130066975:ATAC-STARR-seq lymphoblastoid silent region 13475 [Gene]
LOC130066976:ATAC-STARR-seq lymphoblastoid silent region 13476 [Gene]
LOC130066978:ATAC-STARR-seq lymphoblastoid silent region 13477 [Gene]
LOC130066979:ATAC-STARR-seq lymphoblastoid silent region 13478 [Gene]
LOC130066980:ATAC-STARR-seq lymphoblastoid silent region 13481 [Gene]
LOC130066981:ATAC-STARR-seq lymphoblastoid silent region 13482 [Gene]
LOC130066983:ATAC-STARR-seq lymphoblastoid silent region 13484 [Gene]
LOC130066985:ATAC-STARR-seq lymphoblastoid silent region 13485 [Gene]
LOC130066986:ATAC-STARR-seq lymphoblastoid silent region 13486 [Gene]
LOC130066987:ATAC-STARR-seq lymphoblastoid silent region 13487 [Gene]
LOC130066988:ATAC-STARR-seq lymphoblastoid silent region 13488 [Gene]
LOC130066989:ATAC-STARR-seq lymphoblastoid silent region 13489 [Gene]
LOC130066990:ATAC-STARR-seq lymphoblastoid silent region 13490 [Gene]
LOC130066991:ATAC-STARR-seq lymphoblastoid silent region 13491 [Gene]
LOC130066992:ATAC-STARR-seq lymphoblastoid silent region 13492 [Gene]
LOC130066993:ATAC-STARR-seq lymphoblastoid silent region 13493 [Gene]
LOC130066994:ATAC-STARR-seq lymphoblastoid silent region 13494 [Gene]
LOC126863097:BRD4-independent group 4 enhancer GRCh37_chr22:19220751-19221950 [Gene]
LOC126863098:BRD4-independent group 4 enhancer GRCh37_chr22:19894389-19895588 [Gene]
LOC116309126:CRISPRi-validated cis-regulatory element chr22.250 [Gene]
LOC116309127:CRISPRi-validated cis-regulatory element chr22.431 [Gene]
DGCR8:DGCR8 microprocessor complex subunit [Gene - OMIM - HGNC]
DGCR11:DiGeorge syndrome critical region gene 11 [Gene - HGNC]
DGCR2:DiGeorge syndrome critical region gene 2 [Gene - OMIM - HGNC]
DGCR5:DiGeorge syndrome critical region gene 5 [Gene - OMIM - HGNC]
DGCR6L:DiGeorge syndrome critical region gene 6 like [Gene - OMIM - HGNC]
DGCR6:DiGeorge syndrome critical region gene 6 [Gene - OMIM - HGNC]
GNB1L:G protein subunit beta 1 like [Gene - OMIM - HGNC]
LOC129391263:MPRA-validated peak4453 silencer [Gene]
LOC132090627:Neanderthal introgressed variant-containing enhancer experimental_62558 [Gene]
RANBP1:RAN binding protein 1 [Gene - OMIM - HGNC]
SEPT5-GP1BB:SEPT5-GP1BB readthrough [Gene]
LOC112694764:Sharpr-MPRA regulatory region 10527 [Gene]
LOC125424387:Sharpr-MPRA regulatory region 11316 [Gene]
LOC114004361:Sharpr-MPRA regulatory region 11686 [Gene]
LOC121627929:Sharpr-MPRA regulatory region 13949 [Gene]
LOC125424386:Sharpr-MPRA regulatory region 15144 [Gene]
LOC112694766:Sharpr-MPRA regulatory region 2516 [Gene]
LOC125424388:Sharpr-MPRA regulatory region 9836 [Gene]
TBX1:T-box transcription factor 1 [Gene - OMIM - HGNC]
UFD1-AS1:UFD1 antisense RNA 1 [Gene - HGNC]
LOC110120888:VISTA enhancer hs515 [Gene]
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]
CCDC188:coiled-coil domain containing 188 [Gene - HGNC]
LOC108510655:enhancer-blocking element 22-3 upstream of CCDC188 [Gene]
ESS2:ess-2 splicing factor homolog [Gene - OMIM - HGNC]
FAM230E:family with sequence similarity 230 member E [Gene - HGNC]
FAM230F:family with sequence similarity 230 member F [Gene - HGNC]
FAM246C:family with sequence similarity 246 member C (gene/pseudogene) [Gene - HGNC]
GP1BB:glycoprotein Ib platelet subunit beta [Gene - OMIM - HGNC]
GSC2:goosecoid homeobox 2 [Gene - OMIM - HGNC]
HIRA:histone cell cycle regulator [Gene - OMIM - HGNC]
HSERVPRODH:human-specific endogenous retroviral insert PRODH enhancer [Gene]
LINC01311:long intergenic non-protein coding RNA 1311 [Gene - HGNC]
LINC02891:long intergenic non-protein coding RNA 2891 [Gene - HGNC]
LINC00895:long intergenic non-protein coding RNA 895 [Gene - HGNC]
LINC00896:long intergenic non-protein coding RNA 896 [Gene - HGNC]
MIR1286:microRNA 1286 [Gene - HGNC]
MIR1306:microRNA 1306 [Gene - HGNC]
MIR185:microRNA 185 [Gene - OMIM - HGNC]
MIR3618:microRNA 3618 [Gene - HGNC]
MIR4761:microRNA 4761 [Gene - HGNC]
MIR6816:microRNA 6816 [Gene - HGNC]
MRPL40:mitochondrial ribosomal protein L40 [Gene - OMIM - HGNC]
PRODH:proline dehydrogenase 1 [Gene - OMIM - HGNC]
RTN4R:reticulon 4 receptor [Gene - OMIM - HGNC]
RTL10:retrotransposon Gag like 10 [Gene - OMIM - HGNC]
SEPTIN5:septin 5 [Gene - OMIM - HGNC]
SNORA77B:small nucleolar RNA, H/ACA box 77B [Gene - HGNC]
SLC25A1:solute carrier family 25 member 1 [Gene - OMIM - HGNC]
TRMT2A:tRNA methyltransferase 2 homolog A [Gene - OMIM - HGNC]
TSSK2:testis specific serine kinase 2 [Gene - OMIM - HGNC]
TXNRD2:thioredoxin reductase 2 [Gene - OMIM - HGNC]
TANGO2:transport and golgi organization 2 homolog [Gene - OMIM - HGNC]
UFD1:ubiquitin recognition factor in ER associated degradation 1 [Gene - OMIM - HGNC]
LOC122455341:uncharacterized LOC122455341 [Gene]
ZDHHC8:zinc finger DHHC-type palmitoyltransferase 8 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

GRCh38/hg38 22q11.21(chr22:18718488-20324240)x1

HGVS:

NC_000022.11:g.(?_18718488)_(20324240_?)del
NC_000022.10:g.(?_18706001)_(20311763_?)del
NC_000022.9:g.(?_17086001)_(18691763_?)del

Links:

dbVar: nssv583054; dbVar: nsv533893

Observations:

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

Recent activity

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Xanthomonas surreyensis strain Sa3BUA13 NODE_31_length_1246_cov_57.872541, whole...
Xanthomonas surreyensis strain Sa3BUA13 NODE_31_length_1246_cov_57.872541, whole genome shotgun sequence
gi|1912935339|ref|NZ_JACSQX01000003 gnl|WGS:NZ_JACSQX01|NODE_31_length_1246_cov_57.872541

Nucleotide
NLR family CARD domain-containing protein 4 isoform X1 [Homo sapiens]
NLR family CARD domain-containing protein 4 isoform X1 [Homo sapiens]
gi|2217329958|ref|XP_047301312.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000176664	ISCA site 1 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Pathogenic (Dec 22, 2010)	unknown	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

SCV000176664

ISCA site 1

See additional submitters

no assertion criteria provided

Pathogenic
(Dec 22, 2010)

unknown

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
human	not provided	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]

PMID:: 20466091
PMCID:: PMC2869000

Details of each submission

From ISCA site 1, SCV000176664.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	human	1	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	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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