GRCh38/hg38 2q22.2-22.3(chr2:141666537-147845662)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 12, 2011
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:: RCV000054086.5

Allele description [Variation Report for GRCh38/hg38 2q22.2-22.3(chr2:141666537-147845662)x1]

GRCh38/hg38 2q22.2-22.3(chr2:141666537-147845662)x1

Genes:

ARHGAP15-AS1:ARHGAP15 antisense RNA 1 [Gene - HGNC]
LOC129934864:ATAC-STARR-seq lymphoblastoid active region 16597 [Gene]
LOC129934865:ATAC-STARR-seq lymphoblastoid active region 16598 [Gene]
LOC129934867:ATAC-STARR-seq lymphoblastoid active region 16599 [Gene]
LOC129934868:ATAC-STARR-seq lymphoblastoid active region 16600 [Gene]
LOC129934871:ATAC-STARR-seq lymphoblastoid active region 16601 [Gene]
LOC129934872:ATAC-STARR-seq lymphoblastoid active region 16602 [Gene]
LOC129934874:ATAC-STARR-seq lymphoblastoid active region 16603 [Gene]
LOC129934875:ATAC-STARR-seq lymphoblastoid active region 16606 [Gene]
LOC129934876:ATAC-STARR-seq lymphoblastoid active region 16607 [Gene]
LOC129934878:ATAC-STARR-seq lymphoblastoid active region 16608 [Gene]
LOC129934879:ATAC-STARR-seq lymphoblastoid active region 16609 [Gene]
LOC129934880:ATAC-STARR-seq lymphoblastoid active region 16610 [Gene]
LOC129934881:ATAC-STARR-seq lymphoblastoid active region 16611 [Gene]
LOC129934882:ATAC-STARR-seq lymphoblastoid active region 16612 [Gene]
LOC129934883:ATAC-STARR-seq lymphoblastoid active region 16613 [Gene]
LOC129934866:ATAC-STARR-seq lymphoblastoid silent region 11989 [Gene]
LOC129934869:ATAC-STARR-seq lymphoblastoid silent region 11990 [Gene]
LOC129934870:ATAC-STARR-seq lymphoblastoid silent region 11991 [Gene]
LOC129934873:ATAC-STARR-seq lymphoblastoid silent region 11992 [Gene]
LOC129934877:ATAC-STARR-seq lymphoblastoid silent region 11994 [Gene]
LOC129934884:ATAC-STARR-seq lymphoblastoid silent region 11995 [Gene]
LOC129934885:ATAC-STARR-seq lymphoblastoid silent region 11996 [Gene]
LOC129934886:ATAC-STARR-seq lymphoblastoid silent region 11997 [Gene]
LOC126806360:BRD4-independent group 4 enhancer GRCh37_chr2:142888453-142889652 [Gene]
LOC126806363:BRD4-independent group 4 enhancer GRCh37_chr2:146557300-146558499 [Gene]
LOC126806364:BRD4-independent group 4 enhancer GRCh37_chr2:147391420-147392619 [Gene]
LOC126806365:BRD4-independent group 4 enhancer GRCh37_chr2:148221182-148222381 [Gene]
LOC126806362:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:145764403-145765602 [Gene]
LOC111556162:HNF1 motif-containing MPRA enhancer 151 [Gene]
LRP1B:LDL receptor related protein 1B [Gene - OMIM - HGNC]
LOC126806361:MED14-independent group 3 enhancer GRCh37_chr2:143688223-143689422 [Gene]
LOC129388928:MPRA-validated peak3890 silencer [Gene]
LOC129388929:MPRA-validated peak3893 silencer [Gene]
LOC129388930:MPRA-validated peak3896 silencer [Gene]
LOC132088758:Neanderthal introgressed variant-containing enhancer experimental_53189 [Gene]
ARHGAP15:Rho GTPase activating protein 15 [Gene - OMIM - HGNC]
LOC112806051:Sharpr-MPRA regulatory region 3137 [Gene]
LOC122819163:Sharpr-MPRA regulatory region 4867 [Gene]
LOC122819164:Sharpr-MPRA regulatory region 508 [Gene]
LOC110121209:VISTA enhancer hs1802 [Gene]
LOC110120671:VISTA enhancer hs407 [Gene]
LOC110120706:VISTA enhancer hs568 [Gene]
LOC110120715:VISTA enhancer hs609 [Gene]
LOC110120731:VISTA enhancer hs649 [Gene]
LOC110120740:VISTA enhancer hs675 [Gene]
ZEB2-AS1:ZEB2 antisense RNA 1 [Gene - HGNC]
ACVR2A:activin A receptor type 2A [Gene - OMIM - HGNC]
GTDC1:glycosyltransferase like domain containing 1 [Gene - OMIM - HGNC]
KYNU:kynureninase [Gene - OMIM - HGNC]
LINC01412:long intergenic non-protein coding RNA 1412 [Gene - HGNC]
LINC01911:long intergenic non-protein coding RNA 1911 [Gene - HGNC]
LINC01966:long intergenic non-protein coding RNA 1966 [Gene - HGNC]
LINC02993:long intergenic non-protein coding RNA 2993 [Gene - HGNC]
LOC107228318:origin of replication S3 [Gene]
LOC111721705:skeletal muscle cis-regulatory module overlapping ZEB2 [Gene]
TEX41:testis expressed 41 [Gene - HGNC]
LOC101928386:uncharacterized LOC101928386 [Gene]
ZEB2:zinc finger E-box binding homeobox 2 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

2q22.2-22.3

Genomic location:

Preferred name:

GRCh38/hg38 2q22.2-22.3(chr2:141666537-147845662)x1

HGVS:

NC_000002.12:g.(?_141666537)_(147845662_?)del
NC_000002.10:g.(?_142140576)_(148319701_?)del
NC_000002.11:g.(?_142424106)_(148603231_?)del

Links:

dbVar: nssv577713; dbVar: nsv532754

Observations:

Condition(s)

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

Recent activity

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torsin-1B isoform X1 [Rattus norvegicus]
torsin-1B isoform X1 [Rattus norvegicus]
gi|2678930165|ref|XP_063140030.1|

Protein
RecName: Full=chitinase-like effector; Flags: Precursor
RecName: Full=chitinase-like effector; Flags: Precursor
gi|2778953529|sp|A0A0W0FPC8.1|CHI_M

Protein
UI-R-DQ0-ciz-d-13-0-UI.s1 UI-R-DQ0 Rattus norvegicus cDNA clone UI-R-DQ0-ciz-d-1...
UI-R-DQ0-ciz-d-13-0-UI.s1 UI-R-DQ0 Rattus norvegicus cDNA clone UI-R-DQ0-ciz-d-13-0-UI 3', mRNA sequence
gi|14979519|gnl|dbEST|9106195|gb|BI 9.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000081450	GeneDx	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	not provided	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

SCV000081450

GeneDx

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))

Pathogenic
(Aug 12, 2011)

not provided

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

Citations

PubMed

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]

PMID:: 21844811
PMCID:: PMC3661946

Details of each submission

From GeneDx, SCV000081450.4

#	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	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: Oct 14, 2023

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