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GRCh38/hg38 2q22.3-24.1(chr2:147251948-157856378)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:
RCV000054090.6

Allele description [Variation Report for GRCh38/hg38 2q22.3-24.1(chr2:147251948-157856378)x1]

GRCh38/hg38 2q22.3-24.1(chr2:147251948-157856378)x1

Genes:
  • ARL5A:ADP ribosylation factor like GTPase 5A [Gene - OMIM - HGNC]
  • ARL6IP6:ADP ribosylation factor like GTPase 6 interacting protein 6 [Gene - OMIM - HGNC]
  • LOC129934882:ATAC-STARR-seq lymphoblastoid active region 16612 [Gene]
  • LOC129934883:ATAC-STARR-seq lymphoblastoid active region 16613 [Gene]
  • LOC129934887:ATAC-STARR-seq lymphoblastoid active region 16614 [Gene]
  • LOC129934888:ATAC-STARR-seq lymphoblastoid active region 16615 [Gene]
  • LOC129934889:ATAC-STARR-seq lymphoblastoid active region 16616 [Gene]
  • LOC129934890:ATAC-STARR-seq lymphoblastoid active region 16617 [Gene]
  • LOC129934891:ATAC-STARR-seq lymphoblastoid active region 16618 [Gene]
  • LOC129934892:ATAC-STARR-seq lymphoblastoid active region 16619 [Gene]
  • LOC129934894:ATAC-STARR-seq lymphoblastoid active region 16620 [Gene]
  • LOC129934895:ATAC-STARR-seq lymphoblastoid active region 16621 [Gene]
  • LOC129934897:ATAC-STARR-seq lymphoblastoid active region 16622 [Gene]
  • LOC129934900:ATAC-STARR-seq lymphoblastoid active region 16623 [Gene]
  • LOC129934901:ATAC-STARR-seq lymphoblastoid active region 16624 [Gene]
  • LOC129934902:ATAC-STARR-seq lymphoblastoid active region 16625 [Gene]
  • LOC129934904:ATAC-STARR-seq lymphoblastoid active region 16627 [Gene]
  • LOC129934905:ATAC-STARR-seq lymphoblastoid active region 16628 [Gene]
  • LOC129934907:ATAC-STARR-seq lymphoblastoid active region 16629 [Gene]
  • LOC129934908:ATAC-STARR-seq lymphoblastoid active region 16630 [Gene]
  • LOC129934909:ATAC-STARR-seq lymphoblastoid active region 16631 [Gene]
  • LOC129934910:ATAC-STARR-seq lymphoblastoid active region 16632 [Gene]
  • LOC129934912:ATAC-STARR-seq lymphoblastoid active region 16633 [Gene]
  • LOC129934913:ATAC-STARR-seq lymphoblastoid active region 16634 [Gene]
  • LOC129934914:ATAC-STARR-seq lymphoblastoid active region 16635 [Gene]
  • LOC129934915:ATAC-STARR-seq lymphoblastoid active region 16636 [Gene]
  • LOC129934917:ATAC-STARR-seq lymphoblastoid active region 16639 [Gene]
  • LOC129934920:ATAC-STARR-seq lymphoblastoid active region 16640 [Gene]
  • LOC129934921:ATAC-STARR-seq lymphoblastoid active region 16641 [Gene]
  • LOC129934922:ATAC-STARR-seq lymphoblastoid active region 16642 [Gene]
  • LOC129934923:ATAC-STARR-seq lymphoblastoid active region 16643 [Gene]
  • LOC129934924:ATAC-STARR-seq lymphoblastoid active region 16644 [Gene]
  • LOC129934926:ATAC-STARR-seq lymphoblastoid active region 16645 [Gene]
  • LOC129934927:ATAC-STARR-seq lymphoblastoid active region 16646 [Gene]
  • LOC129934930:ATAC-STARR-seq lymphoblastoid active region 16648 [Gene]
  • LOC129934931:ATAC-STARR-seq lymphoblastoid active region 16649 [Gene]
  • LOC129934932:ATAC-STARR-seq lymphoblastoid active region 16650 [Gene]
  • LOC129934933:ATAC-STARR-seq lymphoblastoid active region 16651 [Gene]
  • LOC129934935:ATAC-STARR-seq lymphoblastoid active region 16655 [Gene]
  • LOC129934936:ATAC-STARR-seq lymphoblastoid active region 16656 [Gene]
  • LOC129934938:ATAC-STARR-seq lymphoblastoid active region 16657 [Gene]
  • LOC129934940:ATAC-STARR-seq lymphoblastoid active region 16658 [Gene]
  • LOC129934942:ATAC-STARR-seq lymphoblastoid active region 16659 [Gene]
  • LOC129934944:ATAC-STARR-seq lymphoblastoid active region 16661 [Gene]
  • LOC129934945:ATAC-STARR-seq lymphoblastoid active region 16662 [Gene]
  • LOC129934946:ATAC-STARR-seq lymphoblastoid active region 16663 [Gene]
  • LOC129934950:ATAC-STARR-seq lymphoblastoid active region 16664 [Gene]
  • LOC129934952:ATAC-STARR-seq lymphoblastoid active region 16665 [Gene]
  • LOC129934953:ATAC-STARR-seq lymphoblastoid active region 16666 [Gene]
  • LOC129934954:ATAC-STARR-seq lymphoblastoid active region 16667 [Gene]
  • LOC129934955:ATAC-STARR-seq lymphoblastoid active region 16668 [Gene]
  • LOC129934956:ATAC-STARR-seq lymphoblastoid active region 16669 [Gene]
  • LOC129934960:ATAC-STARR-seq lymphoblastoid active region 16670 [Gene]
  • LOC129934961:ATAC-STARR-seq lymphoblastoid active region 16671 [Gene]
  • LOC129934962:ATAC-STARR-seq lymphoblastoid active region 16672 [Gene]
  • LOC129934963:ATAC-STARR-seq lymphoblastoid active region 16673 [Gene]
  • LOC129934964:ATAC-STARR-seq lymphoblastoid active region 16674 [Gene]
  • LOC129934965:ATAC-STARR-seq lymphoblastoid active region 16675 [Gene]
  • LOC129934967:ATAC-STARR-seq lymphoblastoid active region 16676 [Gene]
  • LOC129934968:ATAC-STARR-seq lymphoblastoid active region 16677 [Gene]
  • LOC129934969:ATAC-STARR-seq lymphoblastoid active region 16678 [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]
  • LOC129934893:ATAC-STARR-seq lymphoblastoid silent region 12000 [Gene]
  • LOC129934896:ATAC-STARR-seq lymphoblastoid silent region 12001 [Gene]
  • LOC129934898:ATAC-STARR-seq lymphoblastoid silent region 12002 [Gene]
  • LOC129934899:ATAC-STARR-seq lymphoblastoid silent region 12003 [Gene]
  • LOC129934903:ATAC-STARR-seq lymphoblastoid silent region 12004 [Gene]
  • LOC129934906:ATAC-STARR-seq lymphoblastoid silent region 12005 [Gene]
  • LOC129934911:ATAC-STARR-seq lymphoblastoid silent region 12006 [Gene]
  • LOC129934916:ATAC-STARR-seq lymphoblastoid silent region 12007 [Gene]
  • LOC129934918:ATAC-STARR-seq lymphoblastoid silent region 12008 [Gene]
  • LOC129934919:ATAC-STARR-seq lymphoblastoid silent region 12009 [Gene]
  • LOC129934925:ATAC-STARR-seq lymphoblastoid silent region 12010 [Gene]
  • LOC129934928:ATAC-STARR-seq lymphoblastoid silent region 12011 [Gene]
  • LOC129934929:ATAC-STARR-seq lymphoblastoid silent region 12012 [Gene]
  • LOC129934934:ATAC-STARR-seq lymphoblastoid silent region 12013 [Gene]
  • LOC129934937:ATAC-STARR-seq lymphoblastoid silent region 12014 [Gene]
  • LOC129934939:ATAC-STARR-seq lymphoblastoid silent region 12015 [Gene]
  • LOC129934941:ATAC-STARR-seq lymphoblastoid silent region 12016 [Gene]
  • LOC129934943:ATAC-STARR-seq lymphoblastoid silent region 12018 [Gene]
  • LOC129934947:ATAC-STARR-seq lymphoblastoid silent region 12019 [Gene]
  • LOC129934948:ATAC-STARR-seq lymphoblastoid silent region 12020 [Gene]
  • LOC129934949:ATAC-STARR-seq lymphoblastoid silent region 12021 [Gene]
  • LOC129934951:ATAC-STARR-seq lymphoblastoid silent region 12022 [Gene]
  • LOC129934957:ATAC-STARR-seq lymphoblastoid silent region 12024 [Gene]
  • LOC129934958:ATAC-STARR-seq lymphoblastoid silent region 12025 [Gene]
  • LOC129934959:ATAC-STARR-seq lymphoblastoid silent region 12026 [Gene]
  • LOC129934966:ATAC-STARR-seq lymphoblastoid silent region 12027 [Gene]
  • LOC129934970:ATAC-STARR-seq lymphoblastoid silent region 12028 [Gene]
  • LOC129934971:ATAC-STARR-seq lymphoblastoid silent region 12029 [Gene]
  • LOC126806365:BRD4-independent group 4 enhancer GRCh37_chr2:148221182-148222381 [Gene]
  • LOC126806367:BRD4-independent group 4 enhancer GRCh37_chr2:149016781-149017980 [Gene]
  • LOC126806369:BRD4-independent group 4 enhancer GRCh37_chr2:150734031-150735230 [Gene]
  • LOC126806370:BRD4-independent group 4 enhancer GRCh37_chr2:151199972-151201171 [Gene]
  • LOC126806373:BRD4-independent group 4 enhancer GRCh37_chr2:152410007-152411206 [Gene]
  • LOC126806374:BRD4-independent group 4 enhancer GRCh37_chr2:153474731-153475930 [Gene]
  • LOC126806375:BRD4-independent group 4 enhancer GRCh37_chr2:153502126-153503325 [Gene]
  • LOC126806380:BRD4-independent group 4 enhancer GRCh37_chr2:154449049-154450248 [Gene]
  • LOC126806381:BRD4-independent group 4 enhancer GRCh37_chr2:155097618-155098817 [Gene]
  • LOC126806387:BRD4-independent group 4 enhancer GRCh37_chr2:158590437-158591636 [Gene]
  • LOC126806371:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:151476766-151477965 [Gene]
  • LOC126806376:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:153519134-153520333 [Gene]
  • LOC126806382:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:155956194-155957393 [Gene]
  • LOC126806386:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:158320283-158321482 [Gene]
  • LOC115945200:CRISPRi-validated cis-regulatory element chr2.5074 [Gene]
  • GALNT13-AS1:GALNT13 antisense RNA 1 [Gene - HGNC]
  • LOC111556122:HNF1 motif-containing MPRA enhancer 37 [Gene]
  • LYPD6:LY6/PLAUR domain containing 6 [Gene - OMIM - HGNC]
  • LYPD6B:LY6/PLAUR domain containing 6B [Gene - HGNC]
  • LOC126806368:MED14-independent group 3 enhancer GRCh37_chr2:150443500-150444699 [Gene]
  • LOC126806377:MED14-independent group 3 enhancer GRCh37_chr2:153557503-153558702 [Gene]
  • LOC126806378:MED14-independent group 3 enhancer GRCh37_chr2:153702825-153704024 [Gene]
  • LOC126806383:MED14-independent group 3 enhancer GRCh37_chr2:156087204-156088403 [Gene]
  • LOC126806384:MED14-independent group 3 enhancer GRCh37_chr2:156939984-156941183 [Gene]
  • LOC126806388:MED14-independent group 3 enhancer GRCh37_chr2:158694657-158695856 [Gene]
  • MMADHC-DT:MMADHC divergent transcript [Gene - HGNC]
  • LOC129388931:MPRA-validated peak3898 silencer [Gene]
  • LOC129388932:MPRA-validated peak3900 silencer [Gene]
  • LOC129388933:MPRA-validated peak3904 silencer [Gene]
  • LOC129388934:MPRA-validated peak3905 silencer [Gene]
  • LOC129388935:MPRA-validated peak3906 silencer [Gene]
  • NMI:N-myc and STAT interactor [Gene - OMIM - HGNC]
  • LOC108348024:NEB-ARL5A intergenic CAGE-defined B cell enhancer [Gene]
  • LOC132088759:Neanderthal introgressed variant-containing enhancer experimental_53210 [Gene]
  • LOC132088760:Neanderthal introgressed variant-containing enhancer experimental_53218 [Gene]
  • LOC132088761:Neanderthal introgressed variant-containing enhancer experimental_53336 [Gene]
  • LOC126806366:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:148765513-148766712 [Gene]
  • LOC126806372:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:151519399-151520598 [Gene]
  • LOC126806379:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:153925160-153926359 [Gene]
  • LOC126806385:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:158102473-158103672 [Gene]
  • RBM43:RNA binding motif protein 43 [Gene - HGNC]
  • RND3:Rho family GTPase 3 [Gene - OMIM - HGNC]
  • LOC122847298:Sharpr-MPRA regulatory region 11721 [Gene]
  • LOC120961787:Sharpr-MPRA regulatory region 14725 [Gene]
  • LOC122847293:Sharpr-MPRA regulatory region 14986 [Gene]
  • LOC120977009:Sharpr-MPRA regulatory region 15124 [Gene]
  • LOC122819165:Sharpr-MPRA regulatory region 1843 [Gene]
  • LOC112806055:Sharpr-MPRA regulatory region 2662 [Gene]
  • LOC122819167:Sharpr-MPRA regulatory region 317 [Gene]
  • LOC112806054:Sharpr-MPRA regulatory region 4301 [Gene]
  • LOC122847296:Sharpr-MPRA regulatory region 469 [Gene]
  • LOC122847297:Sharpr-MPRA regulatory region 8392 [Gene]
  • LOC122847295:Sharpr-MPRA regulatory region 847 [Gene]
  • LOC122847294:Sharpr-MPRA regulatory region 9612 [Gene]
  • LOC122819166:Sharpr-MPRA regulatory region 9639 [Gene]
  • TNFAIP6:TNF alpha induced protein 6 [Gene - OMIM - HGNC]
  • LOC110121086:VISTA enhancer hs1386 [Gene]
  • LOC110120673:VISTA enhancer hs411 [Gene]
  • LOC110120674:VISTA enhancer hs413 [Gene]
  • LOC110120675:VISTA enhancer hs415 [Gene]
  • LOC110120708:VISTA enhancer hs573 [Gene]
  • LOC110120710:VISTA enhancer hs580 [Gene]
  • LOC110120736:VISTA enhancer hs662 [Gene]
  • ACVR1:activin A receptor type 1 [Gene - OMIM - HGNC]
  • ACVR1C:activin A receptor type 1C [Gene - OMIM - HGNC]
  • ACVR2A:activin A receptor type 2A [Gene - OMIM - HGNC]
  • CACNB4:calcium voltage-gated channel auxiliary subunit beta 4 [Gene - OMIM - HGNC]
  • CYTIP:cytohesin 1 interacting protein [Gene - OMIM - HGNC]
  • EPC2:enhancer of polycomb homolog 2 [Gene - OMIM - HGNC]
  • ERMN:ermin [Gene - OMIM - HGNC]
  • FMNL2:formin like 2 [Gene - OMIM - HGNC]
  • GPD2:glycerol-3-phosphate dehydrogenase 2 [Gene - OMIM - HGNC]
  • KIF5C:kinesin family member 5C [Gene - OMIM - HGNC]
  • LINC01817:long intergenic non-protein coding RNA 1817 [Gene - HGNC]
  • LINC01818:long intergenic non-protein coding RNA 1818 [Gene - HGNC]
  • LINC01876:long intergenic non-protein coding RNA 1876 [Gene - HGNC]
  • LINC01920:long intergenic non-protein coding RNA 1920 [Gene - HGNC]
  • LINC01931:long intergenic non-protein coding RNA 1931 [Gene - HGNC]
  • LINC02612:long intergenic non-protein coding RNA 2612 [Gene - HGNC]
  • MMADHC:metabolism of cobalamin associated D [Gene - OMIM - HGNC]
  • MBD5:methyl-CpG binding domain protein 5 [Gene - OMIM - HGNC]
  • MIR4773-1:microRNA 4773-1 [Gene - HGNC]
  • MIR4773-2:microRNA 4773-2 [Gene - HGNC]
  • MIR9899:microRNA 9899 [Gene - HGNC]
  • NEB:nebulin [Gene - OMIM - HGNC]
  • NR4A2:nuclear receptor subfamily 4 group A member 2 [Gene - OMIM - HGNC]
  • ORC4:origin recognition complex subunit 4 [Gene - OMIM - HGNC]
  • GALNT13:polypeptide N-acetylgalactosaminyltransferase 13 [Gene - OMIM - HGNC]
  • GALNT5:polypeptide N-acetylgalactosaminyltransferase 5 [Gene - OMIM - HGNC]
  • KCNJ3:potassium inwardly rectifying channel subfamily J member 3 [Gene - OMIM - HGNC]
  • PRPF40A:pre-mRNA processing factor 40 homolog A [Gene - OMIM - HGNC]
  • RIF1:replication timing regulatory factor 1 [Gene - OMIM - HGNC]
  • RPRM:reprimo, TP53 dependent G2 arrest mediator homolog [Gene - OMIM - HGNC]
  • STAM2:signal transducing adaptor molecule 2 [Gene - OMIM - HGNC]
  • TRA-CGC3-1:tRNA-Ala (anticodon CGC) 3-1 [Gene - HGNC]
  • TRG-GCC2-2:tRNA-Gly (anticodon GCC) 2-2 [Gene - HGNC]
  • LOC101928553:uncharacterized LOC101928553 [Gene]
  • LOC101929319:uncharacterized LOC101929319 [Gene]
  • FLJ46875:uncharacterized LOC440918 [Gene]
Variant type:
copy number loss
Cytogenetic location:
2q22.3-24.1
Genomic location:
Preferred name:
GRCh38/hg38 2q22.3-24.1(chr2:147251948-157856378)x1
HGVS:
  • NC_000002.12:g.(?_147251948)_(157856378_?)del
  • NC_000002.10:g.(?_147725986)_(158421136_?)del
  • NC_000002.11:g.(?_148009516)_(158712890_?)del
Links:
dbVar: nssv577719; dbVar: nsv532758
Observations:
1

Condition(s)

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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000081454ISCA site 17

See additional submitters

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		not providedclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not providednot providednot providednot providedclinical 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 ISCA site 17, SCV000081454.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providedyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Oct 14, 2023