GRCh38/hg38 22q11.21-11.22(chr22:21454661-22562663)x1 AND See cases

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Sep 16, 2011
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:: RCV000053082.12

Allele description [Variation Report for GRCh38/hg38 22q11.21-11.22(chr22:21454661-22562663)x1]

GRCh38/hg38 22q11.21-11.22(chr22:21454661-22562663)x1

Genes:

LOC130067023:ATAC-STARR-seq lymphoblastoid active region 18698 [Gene]
LOC130067029:ATAC-STARR-seq lymphoblastoid active region 18702 [Gene]
LOC130067030:ATAC-STARR-seq lymphoblastoid active region 18703 [Gene]
LOC130067031:ATAC-STARR-seq lymphoblastoid active region 18704 [Gene]
LOC130067034:ATAC-STARR-seq lymphoblastoid active region 18705 [Gene]
LOC130067035:ATAC-STARR-seq lymphoblastoid active region 18706 [Gene]
LOC130067036:ATAC-STARR-seq lymphoblastoid active region 18707 [Gene]
LOC130067037:ATAC-STARR-seq lymphoblastoid active region 18708 [Gene]
LOC130067038:ATAC-STARR-seq lymphoblastoid active region 18709 [Gene]
LOC130067039:ATAC-STARR-seq lymphoblastoid active region 18710 [Gene]
LOC130067041:ATAC-STARR-seq lymphoblastoid active region 18712 [Gene]
LOC130067043:ATAC-STARR-seq lymphoblastoid active region 18713 [Gene]
LOC130067045:ATAC-STARR-seq lymphoblastoid active region 18714 [Gene]
LOC130067046:ATAC-STARR-seq lymphoblastoid active region 18715 [Gene]
LOC130067047:ATAC-STARR-seq lymphoblastoid active region 18719 [Gene]
LOC130067048:ATAC-STARR-seq lymphoblastoid active region 18720 [Gene]
LOC130067050:ATAC-STARR-seq lymphoblastoid active region 18721 [Gene]
LOC130067051:ATAC-STARR-seq lymphoblastoid active region 18722 [Gene]
LOC130067052:ATAC-STARR-seq lymphoblastoid active region 18723 [Gene]
LOC130067021:ATAC-STARR-seq lymphoblastoid silent region 13507 [Gene]
LOC130067022:ATAC-STARR-seq lymphoblastoid silent region 13508 [Gene]
LOC130067024:ATAC-STARR-seq lymphoblastoid silent region 13509 [Gene]
LOC130067025:ATAC-STARR-seq lymphoblastoid silent region 13510 [Gene]
LOC130067026:ATAC-STARR-seq lymphoblastoid silent region 13511 [Gene]
LOC130067027:ATAC-STARR-seq lymphoblastoid silent region 13512 [Gene]
LOC130067028:ATAC-STARR-seq lymphoblastoid silent region 13513 [Gene]
LOC130067032:ATAC-STARR-seq lymphoblastoid silent region 13514 [Gene]
LOC130067033:ATAC-STARR-seq lymphoblastoid silent region 13515 [Gene]
LOC130067040:ATAC-STARR-seq lymphoblastoid silent region 13517 [Gene]
LOC130067042:ATAC-STARR-seq lymphoblastoid silent region 13519 [Gene]
LOC130067044:ATAC-STARR-seq lymphoblastoid silent region 13520 [Gene]
LOC130067049:ATAC-STARR-seq lymphoblastoid silent region 13522 [Gene]
LOC130067053:ATAC-STARR-seq lymphoblastoid silent region 13523 [Gene]
LOC130067054:ATAC-STARR-seq lymphoblastoid silent region 13524 [Gene]
LOC130067055:ATAC-STARR-seq lymphoblastoid silent region 13525 [Gene]
LOC130067056:ATAC-STARR-seq lymphoblastoid silent region 13526 [Gene]
LOC126863100:BRD4-independent group 4 enhancer GRCh37_chr22:22145734-22146933 [Gene]
LOC126863101:BRD4-independent group 4 enhancer GRCh37_chr22:22874253-22875452 [Gene]
LOC126863099:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:22064332-22065531 [Gene]
TOP3B:DNA topoisomerase III beta [Gene - OMIM - HGNC]
LOC108491837:IGL region enhancer-blocking element 22-2 [Gene]
LOC129391270:MPRA-validated peak4465 silencer [Gene]
LOC129391271:MPRA-validated peak4466 silencer [Gene]
LOC129391272:MPRA-validated peak4467 silencer [Gene]
LOC132090639:Neanderthal introgressed variant-containing enhancer experimental_63007 [Gene]
LOC132090640:Neanderthal introgressed variant-containing enhancer experimental_63076 [Gene]
LOC132090641:Neanderthal introgressed variant-containing enhancer experimental_63111 [Gene]
PPM1F-AS1:PPM1F antisense RNA 1 [Gene - HGNC]
PRAME:PRAME nuclear receptor transcriptional regulator [Gene - OMIM - HGNC]
RIMBP3C:RIMS binding protein 3C [Gene - OMIM - HGNC]
LOC125424389:Sharpr-MPRA regulatory region 10827 [Gene]
LOC121627932:Sharpr-MPRA regulatory region 14215 [Gene]
LOC125424390:Sharpr-MPRA regulatory region 1853 [Gene]
LOC125424391:Sharpr-MPRA regulatory region 5890 [Gene]
LOC112694768:Sharpr-MPRA regulatory region 76 [Gene]
VPREB1:V-set pre-B cell surrogate light chain 1 [Gene - OMIM - HGNC]
LOC110121474:VISTA enhancer hs2026 [Gene]
YDJC:YdjC chitooligosaccharide deacetylase homolog [Gene - OMIM - HGNC]
CCDC116:coiled-coil domain containing 116 [Gene - HGNC]
IGL:immunoglobulin lambda locus [Gene - HGNC]
IGLV1-36:immunoglobulin lambda variable 1-36 [Gene - HGNC]
IGLV1-40:immunoglobulin lambda variable 1-40 [Gene - HGNC]
IGLV1-44:immunoglobulin lambda variable 1-44 [Gene - HGNC]
IGLV1-47:immunoglobulin lambda variable 1-47 [Gene - HGNC]
IGLV1-50:immunoglobulin lambda variable 1-50 (non-functional) [Gene - HGNC]
IGLV1-51:immunoglobulin lambda variable 1-51 [Gene - HGNC]
IGLV10-54:immunoglobulin lambda variable 10-54 [Gene - HGNC]
IGLV11-55:immunoglobulin lambda variable 11-55 (non-functional) [Gene - HGNC]
IGLV4-60:immunoglobulin lambda variable 4-60 [Gene - HGNC]
IGLV4-69:immunoglobulin lambda variable 4-69 [Gene - HGNC]
IGLV5-37:immunoglobulin lambda variable 5-37 [Gene - HGNC]
IGLV5-45:immunoglobulin lambda variable 5-45 [Gene - HGNC]
IGLV5-48:immunoglobulin lambda variable 5-48 (non-functional) [Gene - HGNC]
IGLV5-52:immunoglobulin lambda variable 5-52 [Gene - HGNC]
IGLV6-57:immunoglobulin lambda variable 6-57 [Gene - HGNC]
IGLV7-43:immunoglobulin lambda variable 7-43 [Gene - HGNC]
IGLV7-46:immunoglobulin lambda variable 7-46 [Gene - HGNC]
IGLV8-61:immunoglobulin lambda variable 8-61 [Gene - HGNC]
IGLV9-49:immunoglobulin lambda variable 9-49 [Gene - HGNC]
MIR130B:microRNA 130b [Gene - OMIM - HGNC]
MIR301B:microRNA 301b [Gene - HGNC]
MAPK1:mitogen-activated protein kinase 1 [Gene - OMIM - HGNC]
PPIL2:peptidylprolyl isomerase like 2 [Gene - OMIM - HGNC]
PPM1F:protein phosphatase, Mg2+/Mn2+ dependent 1F [Gene - OMIM - HGNC]
SDF2L1:stromal cell derived factor 2 like 1 [Gene - OMIM - HGNC]
TMEM191C:transmembrane protein 191C [Gene - HGNC]
UBE2L3:ubiquitin conjugating enzyme E2 L3 [Gene - OMIM - HGNC]
LL22NC03-63E9.3:uncharacterized LOC648691 [Gene]
YPEL1:yippee like 1 [Gene - OMIM - HGNC]
ZNF280A:zinc finger protein 280A [Gene - HGNC]
ZNF280B:zinc finger protein 280B [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

22q11.21-11.22

Genomic location:

Preferred name:

GRCh38/hg38 22q11.21-11.22(chr22:21454661-22562663)x1

HGVS:

NC_000022.11:g.(?_21454661)_(22562663_?)del
NC_000022.10:g.(?_21808950)_(22905068_?)del
NC_000022.9:g.(?_20138950)_(21235068_?)del

Links:

dbVar: nssv582259; dbVar: nssv582352; dbVar: nssv584526; dbVar: nsv531772

Observations:

Condition(s)

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

Recent activity

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PREDICTED: Macaca nemestrina DNA dC->dU-editing enzyme APOBEC-3B-like (LOC105464...
PREDICTED: Macaca nemestrina DNA dC->dU-editing enzyme APOBEC-3B-like (LOC105464550), mRNA
gi|1381472252|ref|XM_024787593.1|

Nucleotide
DNA dC->dU-editing enzyme APOBEC-3B [Pan troglodytes]
DNA dC->dU-editing enzyme APOBEC-3B [Pan troglodytes]
gi|575771855|ref|NP_001276568.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000175664	ISCA site 1 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Likely pathogenic (Jan 5, 2011)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000196341	ISCA site 2 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Pathogenic (Sep 16, 2011)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000196342	ISCA site 8 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Pathogenic (Oct 20, 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

SCV000175664

ISCA site 1

See additional submitters

no assertion criteria provided

Likely pathogenic
(Jan 5, 2011)

de novo

clinical testing

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

SCV000196341

ISCA site 2

See additional submitters

no assertion criteria provided

Pathogenic
(Sep 16, 2011)

de novo

clinical testing

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

SCV000196342

ISCA site 8

See additional submitters

no assertion criteria provided

Pathogenic
(Oct 20, 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
not provided	de novo	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	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, SCV000175664.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	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	de novo	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

From ISCA site 2, SCV000196341.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	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	de novo	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

From ISCA site 8, SCV000196342.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	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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