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GRCh38/hg38 2q31.1-31.2(chr2:171513047-177854080)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 18, 2012
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:
RCV000139646.6

Allele description [Variation Report for GRCh38/hg38 2q31.1-31.2(chr2:171513047-177854080)x1]

GRCh38/hg38 2q31.1-31.2(chr2:171513047-177854080)x1

Genes:
  • LOC129935103:ATAC-STARR-seq lymphoblastoid active region 16758 [Gene]
  • LOC129935106:ATAC-STARR-seq lymphoblastoid active region 16759 [Gene]
  • LOC129935107:ATAC-STARR-seq lymphoblastoid active region 16760 [Gene]
  • LOC129935109:ATAC-STARR-seq lymphoblastoid active region 16761 [Gene]
  • LOC129935113:ATAC-STARR-seq lymphoblastoid active region 16763 [Gene]
  • LOC129935117:ATAC-STARR-seq lymphoblastoid active region 16764 [Gene]
  • LOC129935118:ATAC-STARR-seq lymphoblastoid active region 16765 [Gene]
  • LOC129935119:ATAC-STARR-seq lymphoblastoid active region 16767 [Gene]
  • LOC129935121:ATAC-STARR-seq lymphoblastoid active region 16768 [Gene]
  • LOC129935124:ATAC-STARR-seq lymphoblastoid active region 16769 [Gene]
  • LOC129935128:ATAC-STARR-seq lymphoblastoid active region 16770 [Gene]
  • LOC129935132:ATAC-STARR-seq lymphoblastoid active region 16772 [Gene]
  • LOC129935134:ATAC-STARR-seq lymphoblastoid active region 16774 [Gene]
  • LOC129935135:ATAC-STARR-seq lymphoblastoid active region 16775 [Gene]
  • LOC129935137:ATAC-STARR-seq lymphoblastoid active region 16776 [Gene]
  • LOC129935138:ATAC-STARR-seq lymphoblastoid active region 16777 [Gene]
  • LOC129935139:ATAC-STARR-seq lymphoblastoid active region 16778 [Gene]
  • LOC129935140:ATAC-STARR-seq lymphoblastoid active region 16779 [Gene]
  • LOC129935141:ATAC-STARR-seq lymphoblastoid active region 16780 [Gene]
  • LOC129935142:ATAC-STARR-seq lymphoblastoid active region 16781 [Gene]
  • LOC129935143:ATAC-STARR-seq lymphoblastoid active region 16782 [Gene]
  • LOC129935144:ATAC-STARR-seq lymphoblastoid active region 16783 [Gene]
  • LOC129935145:ATAC-STARR-seq lymphoblastoid active region 16784 [Gene]
  • LOC129935146:ATAC-STARR-seq lymphoblastoid active region 16785 [Gene]
  • LOC129935149:ATAC-STARR-seq lymphoblastoid active region 16786 [Gene]
  • LOC129935154:ATAC-STARR-seq lymphoblastoid active region 16787 [Gene]
  • LOC129935156:ATAC-STARR-seq lymphoblastoid active region 16788 [Gene]
  • LOC129935157:ATAC-STARR-seq lymphoblastoid active region 16789 [Gene]
  • LOC129935159:ATAC-STARR-seq lymphoblastoid active region 16790 [Gene]
  • LOC129935160:ATAC-STARR-seq lymphoblastoid active region 16791 [Gene]
  • LOC129935164:ATAC-STARR-seq lymphoblastoid active region 16792 [Gene]
  • LOC129935166:ATAC-STARR-seq lymphoblastoid active region 16793 [Gene]
  • LOC129935167:ATAC-STARR-seq lymphoblastoid active region 16794 [Gene]
  • LOC129935170:ATAC-STARR-seq lymphoblastoid active region 16796 [Gene]
  • LOC129935173:ATAC-STARR-seq lymphoblastoid active region 16798 [Gene]
  • LOC129935174:ATAC-STARR-seq lymphoblastoid active region 16799 [Gene]
  • LOC129935175:ATAC-STARR-seq lymphoblastoid active region 16800 [Gene]
  • LOC129935104:ATAC-STARR-seq lymphoblastoid silent region 12103 [Gene]
  • LOC129935105:ATAC-STARR-seq lymphoblastoid silent region 12104 [Gene]
  • LOC129935108:ATAC-STARR-seq lymphoblastoid silent region 12106 [Gene]
  • LOC129935110:ATAC-STARR-seq lymphoblastoid silent region 12108 [Gene]
  • LOC129935111:ATAC-STARR-seq lymphoblastoid silent region 12109 [Gene]
  • LOC129935112:ATAC-STARR-seq lymphoblastoid silent region 12110 [Gene]
  • LOC129935114:ATAC-STARR-seq lymphoblastoid silent region 12111 [Gene]
  • LOC129935115:ATAC-STARR-seq lymphoblastoid silent region 12112 [Gene]
  • LOC129935116:ATAC-STARR-seq lymphoblastoid silent region 12113 [Gene]
  • LOC129935120:ATAC-STARR-seq lymphoblastoid silent region 12115 [Gene]
  • LOC129935122:ATAC-STARR-seq lymphoblastoid silent region 12116 [Gene]
  • LOC129935123:ATAC-STARR-seq lymphoblastoid silent region 12117 [Gene]
  • LOC129935125:ATAC-STARR-seq lymphoblastoid silent region 12120 [Gene]
  • LOC129935126:ATAC-STARR-seq lymphoblastoid silent region 12121 [Gene]
  • LOC129935127:ATAC-STARR-seq lymphoblastoid silent region 12122 [Gene]
  • LOC129935129:ATAC-STARR-seq lymphoblastoid silent region 12123 [Gene]
  • LOC129935130:ATAC-STARR-seq lymphoblastoid silent region 12124 [Gene]
  • LOC129935131:ATAC-STARR-seq lymphoblastoid silent region 12125 [Gene]
  • LOC129935133:ATAC-STARR-seq lymphoblastoid silent region 12126 [Gene]
  • LOC129935136:ATAC-STARR-seq lymphoblastoid silent region 12127 [Gene]
  • LOC129935147:ATAC-STARR-seq lymphoblastoid silent region 12128 [Gene]
  • LOC129935148:ATAC-STARR-seq lymphoblastoid silent region 12129 [Gene]
  • LOC129935150:ATAC-STARR-seq lymphoblastoid silent region 12130 [Gene]
  • LOC129935151:ATAC-STARR-seq lymphoblastoid silent region 12131 [Gene]
  • LOC129935152:ATAC-STARR-seq lymphoblastoid silent region 12132 [Gene]
  • LOC129935153:ATAC-STARR-seq lymphoblastoid silent region 12133 [Gene]
  • LOC129935155:ATAC-STARR-seq lymphoblastoid silent region 12134 [Gene]
  • LOC129935158:ATAC-STARR-seq lymphoblastoid silent region 12136 [Gene]
  • LOC129935161:ATAC-STARR-seq lymphoblastoid silent region 12138 [Gene]
  • LOC129935162:ATAC-STARR-seq lymphoblastoid silent region 12139 [Gene]
  • LOC129935163:ATAC-STARR-seq lymphoblastoid silent region 12140 [Gene]
  • LOC129935165:ATAC-STARR-seq lymphoblastoid silent region 12141 [Gene]
  • LOC129935168:ATAC-STARR-seq lymphoblastoid silent region 12143 [Gene]
  • LOC129935169:ATAC-STARR-seq lymphoblastoid silent region 12145 [Gene]
  • LOC129935171:ATAC-STARR-seq lymphoblastoid silent region 12146 [Gene]
  • LOC129935172:ATAC-STARR-seq lymphoblastoid silent region 12147 [Gene]
  • ATP5MC3:ATP synthase membrane subunit c locus 3 [Gene - OMIM - HGNC]
  • LOC126806405:BRD4-independent group 4 enhancer GRCh37_chr2:173295051-173296250 [Gene]
  • LOC126806416:BRD4-independent group 4 enhancer GRCh37_chr2:178051754-178052953 [Gene]
  • LOC126806418:BRD4-independent group 4 enhancer GRCh37_chr2:178202734-178203933 [Gene]
  • LOC126806406:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:173607526-173608725 [Gene]
  • LOC126806411:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:176342216-176343415 [Gene]
  • LOC126806412:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:176651769-176652968 [Gene]
  • LOC126806413:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:177453489-177454688 [Gene]
  • LOC115945201:CRISPRi-validated cis-regulatory element chr2.5458 [Gene]
  • DLX2-DT:DLX2 divergent transcript [Gene - HGNC]
  • GPR155:G protein-coupled receptor 155 [Gene - HGNC]
  • GPR155-DT:GPR155 divergent transcript [Gene - HGNC]
  • HAGLROS:HAGLR opposite strand lncRNA [Gene - HGNC]
  • HAGLR:HOXD antisense growth-associated long non-coding RNA [Gene - OMIM - HGNC]
  • HOXD-AS2:HOXD cluster antisense RNA 2 [Gene - HGNC]
  • ITGA6-AS1:ITGA6 antisense RNA 1 [Gene - HGNC]
  • MAP3K20-AS1:MAP3K20 antisense RNA 1 [Gene - HGNC]
  • LOC126806407:MED14-independent group 3 enhancer GRCh37_chr2:174164665-174165864 [Gene]
  • LOC126806409:MED14-independent group 3 enhancer GRCh37_chr2:174916218-174917417 [Gene]
  • LOC126806410:MED14-independent group 3 enhancer GRCh37_chr2:175778728-175779927 [Gene]
  • LOC126806415:MED14-independent group 3 enhancer GRCh37_chr2:178034228-178035427 [Gene]
  • LOC126806417:MED14-independent group 3 enhancer GRCh37_chr2:178127429-178128628 [Gene]
  • LOC126806419:MED14-independent group 3 enhancer GRCh37_chr2:178338764-178339963 [Gene]
  • LOC129388944:MPRA-validated peak3925 silencer [Gene]
  • LOC129388945:MPRA-validated peak3928 silencer [Gene]
  • LOC129388946:MPRA-validated peak3933 silencer [Gene]
  • LOC129388947:MPRA-validated peak3936 silencer [Gene]
  • LOC129388948:MPRA-validated peak3937 silencer [Gene]
  • LOC129388949:MPRA-validated peak3938 silencer [Gene]
  • LOC129388950:MPRA-validated peak3940 silencer [Gene]
  • LOC129388951:MPRA-validated peak3942 silencer [Gene]
  • LOC129388952:MPRA-validated peak3944 silencer [Gene]
  • LOC129388953:MPRA-validated peak3945 silencer [Gene]
  • LOC129388954:MPRA-validated peak3947 silencer [Gene]
  • NFE2L2:NFE2 like bZIP transcription factor 2 [Gene - OMIM - HGNC]
  • NRAL:NRF2 regulation associated lncRNA [Gene - HGNC]
  • LOC107126359:NUP98-HOXD13 recombination region [Gene]
  • LOC132088795:Neanderthal introgressed variant-containing enhancer experimental_55951 [Gene]
  • LOC132088796:Neanderthal introgressed variant-containing enhancer experimental_56026 [Gene]
  • LOC132088797:Neanderthal introgressed variant-containing enhancer experimental_56072 [Gene]
  • LOC132090686:Neanderthal introgressed variant-containing enhancer experimental_56189 [Gene]
  • LOC132088798:Neanderthal introgressed variant-containing enhancer experimental_56221 [Gene]
  • LOC132090687:Neanderthal introgressed variant-containing enhancer experimental_56231 [Gene]
  • LOC132088799:Neanderthal introgressed variant-containing enhancer experimental_56260 [Gene]
  • LOC132088800:Neanderthal introgressed variant-containing enhancer experimental_56279 [Gene]
  • LOC132088801:Neanderthal introgressed variant-containing enhancer experimental_56293 [Gene]
  • LOC132088802:Neanderthal introgressed variant-containing enhancer experimental_56377 [Gene]
  • LOC132088803:Neanderthal introgressed variant-containing enhancer experimental_56397 [Gene]
  • LOC132088804:Neanderthal introgressed variant-containing enhancer experimental_56479 [Gene]
  • OLA1:Obg like ATPase 1 [Gene - OMIM - HGNC]
  • LOC126806404:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:173117619-173118818 [Gene]
  • LOC126806408:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:174888471-174889670 [Gene]
  • LOC126806414:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:177485641-177486840 [Gene]
  • PDE11A-AS1:PDE11A antisense RNA 1 [Gene - HGNC]
  • PDK1-AS1:PDK1 and ITGA6 antisense RNA 1 [Gene - HGNC]
  • LOC100130691:Putative uncharacterized protein FLJ44553 [Gene]
  • RAPGEF4-AS1:RAPGEF4 antisense RNA 1 [Gene - HGNC]
  • RAPGEF4:Rap guanine nucleotide exchange factor 4 [Gene - OMIM - HGNC]
  • LOC122861240:Sharpr-MPRA regulatory region 126 [Gene]
  • LOC122861249:Sharpr-MPRA regulatory region 13302 [Gene]
  • LOC122861244:Sharpr-MPRA regulatory region 13906 [Gene]
  • LOC122861242:Sharpr-MPRA regulatory region 13988 [Gene]
  • LOC122861253:Sharpr-MPRA regulatory region 14377 [Gene]
  • LOC122861243:Sharpr-MPRA regulatory region 14969 [Gene]
  • LOC122847318:Sharpr-MPRA regulatory region 14975 [Gene]
  • LOC122861247:Sharpr-MPRA regulatory region 15219 [Gene]
  • LOC122861254:Sharpr-MPRA regulatory region 15369 [Gene]
  • LOC122861246:Sharpr-MPRA regulatory region 1697 [Gene]
  • LOC122861252:Sharpr-MPRA regulatory region 2066 [Gene]
  • LOC120977016:Sharpr-MPRA regulatory region 4096 [Gene]
  • LOC122847317:Sharpr-MPRA regulatory region 4152 [Gene]
  • LOC112806059:Sharpr-MPRA regulatory region 4236 [Gene]
  • LOC120977015:Sharpr-MPRA regulatory region 431 [Gene]
  • LOC122861251:Sharpr-MPRA regulatory region 4724 [Gene]
  • LOC112806061:Sharpr-MPRA regulatory region 4751 [Gene]
  • LOC122847320:Sharpr-MPRA regulatory region 7042 [Gene]
  • LOC122861241:Sharpr-MPRA regulatory region 8106 [Gene]
  • LOC112806060:Sharpr-MPRA regulatory region 8299 [Gene]
  • LOC122861248:Sharpr-MPRA regulatory region 8538 [Gene]
  • LOC122861245:Sharpr-MPRA regulatory region 9658 [Gene]
  • LOC122861250:Sharpr-MPRA regulatory region 9735 [Gene]
  • LOC122847319:Sharpr-MPRA regulatory region 994 [Gene]
  • SP3:Sp3 transcription factor [Gene - OMIM - HGNC]
  • SP9:Sp9 transcription factor [Gene - HGNC]
  • LOC110120624:VISTA enhancer hs242 [Gene]
  • LOC110120625:VISTA enhancer hs243 [Gene]
  • LOC110120626:VISTA enhancer hs244 [Gene]
  • LOC110120627:VISTA enhancer hs246 [Gene]
  • LOC110120628:VISTA enhancer hs248 [Gene]
  • LOC110120678:VISTA enhancer hs422 [Gene]
  • LOC110120701:VISTA enhancer hs553 [Gene]
  • LOC110120730:VISTA enhancer hs646 [Gene]
  • LOC110120790:VISTA enhancer hs860 [Gene]
  • LOC110120809:VISTA enhancer hs953 [Gene]
  • WIPF1:WAS/WASL interacting protein family member 1 [Gene - OMIM - HGNC]
  • ATF2:activating transcription factor 2 [Gene - OMIM - HGNC]
  • AGPS:alkylglycerone phosphate synthase [Gene - OMIM - HGNC]
  • CDCA7:cell division cycle associated 7 [Gene - OMIM - HGNC]
  • CHN1:chimerin 1 [Gene - OMIM - HGNC]
  • CHRNA1:cholinergic receptor nicotinic alpha 1 subunit [Gene - OMIM - HGNC]
  • CIR1:corepressor interacting with RBPJ, CIR1 [Gene - OMIM - HGNC]
  • CYBRD1:cytochrome b reductase 1 [Gene - OMIM - HGNC]
  • DLX1:distal-less homeobox 1 [Gene - OMIM - HGNC]
  • DLX2:distal-less homeobox 2 [Gene - OMIM - HGNC]
  • DYNC1I2:dynein cytoplasmic 1 intermediate chain 2 [Gene - OMIM - HGNC]
  • EVX2:even-skipped homeobox 2 [Gene - OMIM - HGNC]
  • HNRNPA3:heterogeneous nuclear ribonucleoprotein A3 [Gene - OMIM - HGNC]
  • HAT1:histone acetyltransferase 1 [Gene - OMIM - HGNC]
  • HOXD10:homeobox D10 [Gene - OMIM - HGNC]
  • HOXD11:homeobox D11 [Gene - OMIM - HGNC]
  • HOXD12:homeobox D12 [Gene - OMIM - HGNC]
  • HOXD13:homeobox D13 [Gene - OMIM - HGNC]
  • HOXD1:homeobox D1 [Gene - OMIM - HGNC]
  • HOXD3:homeobox D3 [Gene - OMIM - HGNC]
  • HOXD4:homeobox D4 [Gene - OMIM - HGNC]
  • HOXD8:homeobox D8 [Gene - OMIM - HGNC]
  • HOXD9:homeobox D9 [Gene - OMIM - HGNC]
  • ITGA6:integrin subunit alpha 6 [Gene - OMIM - HGNC]
  • IFT70A:intraflagellar transport 70A [Gene - OMIM - HGNC]
  • IFT70B:intraflagellar transport 70B [Gene - OMIM - HGNC]
  • LINC01116:long intergenic non-protein coding RNA 1116 [Gene - HGNC]
  • LINC01117:long intergenic non-protein coding RNA 1117 [Gene - HGNC]
  • LINC01305:long intergenic non-protein coding RNA 1305 [Gene - HGNC]
  • LINC01960:long intergenic non-protein coding RNA 1960 [Gene - HGNC]
  • LNPK:lunapark, ER junction formation factor [Gene - OMIM - HGNC]
  • MTX2:metaxin 2 [Gene - OMIM - HGNC]
  • METAP1D:methionyl aminopeptidase type 1D, mitochondrial [Gene - OMIM - HGNC]
  • MIR10B:microRNA 10b [Gene - OMIM - HGNC]
  • MIR1246:microRNA 1246 [Gene - HGNC]
  • MIR3128:microRNA 3128 [Gene - HGNC]
  • MIR4444-1:microRNA 4444-1 [Gene - HGNC]
  • MIR6512:microRNA 6512 [Gene - HGNC]
  • MIR7704:microRNA 7704 [Gene - HGNC]
  • MIR933:microRNA 933 [Gene - HGNC]
  • MAP3K20:mitogen-activated protein kinase kinase kinase 20 [Gene - OMIM - HGNC]
  • PDE11A:phosphodiesterase 11A [Gene - OMIM - HGNC]
  • PDK1:pyruvate dehydrogenase kinase 1 [Gene - OMIM - HGNC]
  • SCRN3:secernin 3 [Gene - OMIM - HGNC]
  • SLC25A12:solute carrier family 25 member 12 [Gene - OMIM - HGNC]
  • LOC100129455:uncharacterized LOC100129455 [Gene]
  • LOC105373757:uncharacterized LOC105373757 [Gene]
  • LOC105373759:uncharacterized LOC105373759 [Gene]
  • LOC401021:uncharacterized LOC401021 [Gene]
Variant type:
copy number loss
Cytogenetic location:
2q31.1-31.2
Genomic location:
Preferred name:
GRCh38/hg38 2q31.1-31.2(chr2:171513047-177854080)x1
HGVS:
  • NC_000002.12:g.(?_171513047)_(177854080_?)del
  • NC_000002.10:g.(?_172077803)_(178427053_?)del
  • NC_000002.11:g.(?_172369557)_(178718807_?)del
Links:
dbVar: nssv1605201; dbVar: nsv917150
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000180231ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Jun 18, 2012) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
humannot providedyes1not providednot providednot providednot providedclinical 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, SCV000180231.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1human1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024