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GRCh38/hg38 12p13.33-13.32(chr12:54427-4004912)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 3, 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:
RCV000140991.6

Allele description [Variation Report for GRCh38/hg38 12p13.33-13.32(chr12:54427-4004912)x1]

GRCh38/hg38 12p13.33-13.32(chr12:54427-4004912)x1

Genes:
  • LOC130007133:ATAC-STARR-seq lymphoblastoid active region 5777 [Gene]
  • LOC130007134:ATAC-STARR-seq lymphoblastoid active region 5778 [Gene]
  • LOC130007137:ATAC-STARR-seq lymphoblastoid active region 5779 [Gene]
  • LOC130007138:ATAC-STARR-seq lymphoblastoid active region 5780 [Gene]
  • LOC130007139:ATAC-STARR-seq lymphoblastoid active region 5781 [Gene]
  • LOC130007142:ATAC-STARR-seq lymphoblastoid active region 5782 [Gene]
  • LOC130007143:ATAC-STARR-seq lymphoblastoid active region 5783 [Gene]
  • LOC130007144:ATAC-STARR-seq lymphoblastoid active region 5784 [Gene]
  • LOC130007145:ATAC-STARR-seq lymphoblastoid active region 5785 [Gene]
  • LOC130007146:ATAC-STARR-seq lymphoblastoid active region 5786 [Gene]
  • LOC130007147:ATAC-STARR-seq lymphoblastoid active region 5787 [Gene]
  • LOC130007148:ATAC-STARR-seq lymphoblastoid active region 5788 [Gene]
  • LOC130007149:ATAC-STARR-seq lymphoblastoid active region 5789 [Gene]
  • LOC130007150:ATAC-STARR-seq lymphoblastoid active region 5790 [Gene]
  • LOC130007151:ATAC-STARR-seq lymphoblastoid active region 5791 [Gene]
  • LOC130007152:ATAC-STARR-seq lymphoblastoid active region 5792 [Gene]
  • LOC130007154:ATAC-STARR-seq lymphoblastoid active region 5795 [Gene]
  • LOC130007155:ATAC-STARR-seq lymphoblastoid active region 5796 [Gene]
  • LOC130007156:ATAC-STARR-seq lymphoblastoid active region 5797 [Gene]
  • LOC130007159:ATAC-STARR-seq lymphoblastoid active region 5798 [Gene]
  • LOC130007160:ATAC-STARR-seq lymphoblastoid active region 5799 [Gene]
  • LOC130007161:ATAC-STARR-seq lymphoblastoid active region 5800 [Gene]
  • LOC130007162:ATAC-STARR-seq lymphoblastoid active region 5801 [Gene]
  • LOC130007163:ATAC-STARR-seq lymphoblastoid active region 5802 [Gene]
  • LOC130007164:ATAC-STARR-seq lymphoblastoid active region 5803 [Gene]
  • LOC130007165:ATAC-STARR-seq lymphoblastoid active region 5804 [Gene]
  • LOC130007167:ATAC-STARR-seq lymphoblastoid active region 5805 [Gene]
  • LOC130007169:ATAC-STARR-seq lymphoblastoid active region 5808 [Gene]
  • LOC130007172:ATAC-STARR-seq lymphoblastoid active region 5809 [Gene]
  • LOC130007173:ATAC-STARR-seq lymphoblastoid active region 5810 [Gene]
  • LOC130007174:ATAC-STARR-seq lymphoblastoid active region 5811 [Gene]
  • LOC130007176:ATAC-STARR-seq lymphoblastoid active region 5812 [Gene]
  • LOC130007177:ATAC-STARR-seq lymphoblastoid active region 5813 [Gene]
  • LOC130007180:ATAC-STARR-seq lymphoblastoid active region 5814 [Gene]
  • LOC130007186:ATAC-STARR-seq lymphoblastoid active region 5816 [Gene]
  • LOC130007190:ATAC-STARR-seq lymphoblastoid active region 5817 [Gene]
  • LOC130007132:ATAC-STARR-seq lymphoblastoid silent region 4100 [Gene]
  • LOC130007135:ATAC-STARR-seq lymphoblastoid silent region 4102 [Gene]
  • LOC130007136:ATAC-STARR-seq lymphoblastoid silent region 4103 [Gene]
  • LOC130007140:ATAC-STARR-seq lymphoblastoid silent region 4104 [Gene]
  • LOC130007141:ATAC-STARR-seq lymphoblastoid silent region 4105 [Gene]
  • LOC130007153:ATAC-STARR-seq lymphoblastoid silent region 4110 [Gene]
  • LOC130007157:ATAC-STARR-seq lymphoblastoid silent region 4112 [Gene]
  • LOC130007158:ATAC-STARR-seq lymphoblastoid silent region 4113 [Gene]
  • LOC130007166:ATAC-STARR-seq lymphoblastoid silent region 4115 [Gene]
  • LOC130007168:ATAC-STARR-seq lymphoblastoid silent region 4116 [Gene]
  • LOC130007170:ATAC-STARR-seq lymphoblastoid silent region 4118 [Gene]
  • LOC130007171:ATAC-STARR-seq lymphoblastoid silent region 4119 [Gene]
  • LOC130007175:ATAC-STARR-seq lymphoblastoid silent region 4122 [Gene]
  • LOC130007178:ATAC-STARR-seq lymphoblastoid silent region 4127 [Gene]
  • LOC130007179:ATAC-STARR-seq lymphoblastoid silent region 4128 [Gene]
  • LOC130007181:ATAC-STARR-seq lymphoblastoid silent region 4129 [Gene]
  • LOC130007182:ATAC-STARR-seq lymphoblastoid silent region 4131 [Gene]
  • LOC130007183:ATAC-STARR-seq lymphoblastoid silent region 4132 [Gene]
  • LOC130007184:ATAC-STARR-seq lymphoblastoid silent region 4134 [Gene]
  • LOC130007185:ATAC-STARR-seq lymphoblastoid silent region 4135 [Gene]
  • LOC130007187:ATAC-STARR-seq lymphoblastoid silent region 4136 [Gene]
  • LOC130007188:ATAC-STARR-seq lymphoblastoid silent region 4138 [Gene]
  • LOC130007189:ATAC-STARR-seq lymphoblastoid silent region 4139 [Gene]
  • LOC130007191:ATAC-STARR-seq lymphoblastoid silent region 4140 [Gene]
  • LOC130007192:ATAC-STARR-seq lymphoblastoid silent region 4141 [Gene]
  • LOC130007193:ATAC-STARR-seq lymphoblastoid silent region 4142 [Gene]
  • LOC130007194:ATAC-STARR-seq lymphoblastoid silent region 4143 [Gene]
  • LOC126861414:BRD4-independent group 4 enhancer GRCh37_chr12:1597926-1599125 [Gene]
  • LOC126861418:BRD4-independent group 4 enhancer GRCh37_chr12:2660049-2661248 [Gene]
  • LOC126861419:BRD4-independent group 4 enhancer GRCh37_chr12:2905599-2906798 [Gene]
  • LOC126861420:BRD4-independent group 4 enhancer GRCh37_chr12:3421757-3422956 [Gene]
  • LOC126861421:BRD4-independent group 4 enhancer GRCh37_chr12:3443867-3445066 [Gene]
  • LOC126861410:BRD4-independent group 4 enhancer GRCh37_chr12:415875-417074 [Gene]
  • CACNA1C-AS1:CACNA1C antisense RNA 1 [Gene - HGNC]
  • CACNA1C-AS2:CACNA1C antisense RNA 2 [Gene - HGNC]
  • CACNA1C-AS4:CACNA1C antisense RNA 4 [Gene - HGNC]
  • CACNA1C-IT1:CACNA1C intronic transcript 1 [Gene - HGNC]
  • CACNA1C-IT2:CACNA1C intronic transcript 2 [Gene - HGNC]
  • CACNA1C-IT3:CACNA1C intronic transcript 3 [Gene - HGNC]
  • LOC126861413:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:1224566-1225765 [Gene]
  • LOC116268425:CRISPRi-validated cis-regulatory element chr12.51 [Gene]
  • ERC1:ELKS/RAB6-interacting/CAST family member 1 [Gene - OMIM - HGNC]
  • FBXL14:F-box and leucine rich repeat protein 14 [Gene - OMIM - HGNC]
  • FKBP4:FKBP prolyl isomerase 4 [Gene - OMIM - HGNC]
  • IQSEC3:IQ motif and Sec7 domain ArfGEF 3 [Gene - OMIM - HGNC]
  • IQSEC3-AS1:IQSEC3 antisense RNA 1 [Gene - HGNC]
  • IQSEC3-AS2:IQSEC3 antisense RNA 2 [Gene - HGNC]
  • ITFG2-AS1:ITFG2 antisense RNA 1 [Gene - HGNC]
  • LOC126861415:MED14-independent group 3 enhancer GRCh37_chr12:1608954-1610153 [Gene]
  • LOC126861416:MED14-independent group 3 enhancer GRCh37_chr12:2063223-2064422 [Gene]
  • LOC126861417:MED14-independent group 3 enhancer GRCh37_chr12:2629110-2630309 [Gene]
  • LOC126861411:MED14-independent group 3 enhancer GRCh37_chr12:754531-755730 [Gene]
  • LOC129390385:MPRA-validated peak1534 silencer [Gene]
  • NINJ2-AS1:NINJ2 antisense RNA 1 [Gene - HGNC]
  • LOC126861412:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:1023012-1024211 [Gene]
  • PARP11-AS1:PARP11 antisense RNA 1 [Gene - HGNC]
  • RAD52:RAD52 homolog, DNA repair protein [Gene - OMIM - HGNC]
  • RHNO1:RAD9-HUS1-RAD1 interacting nuclear orphan 1 [Gene - OMIM - HGNC]
  • SLC6A12-AS1:SLC6A12 antisense RNA 1 [Gene - HGNC]
  • LOC124625880:Sharpr-MPRA regulatory region 10568 [Gene]
  • LOC121403743:Sharpr-MPRA regulatory region 10584 [Gene]
  • LOC121392956:Sharpr-MPRA regulatory region 13344 [Gene]
  • LOC124625885:Sharpr-MPRA regulatory region 1542 [Gene]
  • LOC124625876:Sharpr-MPRA regulatory region 2537 [Gene]
  • LOC124625879:Sharpr-MPRA regulatory region 2999 [Gene]
  • LOC124625878:Sharpr-MPRA regulatory region 3814 [Gene]
  • LOC112163597:Sharpr-MPRA regulatory region 4015 [Gene]
  • LOC112163604:Sharpr-MPRA regulatory region 4380 [Gene]
  • LOC112136100:Sharpr-MPRA regulatory region 5038 [Gene]
  • LOC124625881:Sharpr-MPRA regulatory region 515 [Gene]
  • LOC124625877:Sharpr-MPRA regulatory region 6010 [Gene]
  • LOC121392955:Sharpr-MPRA regulatory region 6322 [Gene]
  • LOC121832825:Sharpr-MPRA regulatory region 6988 [Gene]
  • LOC124625883:Sharpr-MPRA regulatory region 7040 [Gene]
  • LOC124625884:Sharpr-MPRA regulatory region 741 [Gene]
  • LOC124625882:Sharpr-MPRA regulatory region 8339 [Gene]
  • TEAD4:TEA domain transcription factor 4 [Gene - OMIM - HGNC]
  • TSPAN9-IT1:TSPAN9 intronic transcript 1 [Gene - HGNC]
  • TULP3:TUB like protein 3 [Gene - OMIM - HGNC]
  • WNK1:WNK lysine deficient protein kinase 1 [Gene - OMIM - HGNC]
  • WNT5B:Wnt family member 5B [Gene - OMIM - HGNC]
  • ADIPOR2:adiponectin receptor 2 [Gene - OMIM - HGNC]
  • B4GALNT3:beta-1,4-N-acetyl-galactosaminyltransferase 3 [Gene - OMIM - HGNC]
  • CRACR2A:calcium release activated channel regulator 2A [Gene - OMIM - HGNC]
  • CACNA2D4:calcium voltage-gated channel auxiliary subunit alpha2delta 4 [Gene - OMIM - HGNC]
  • CACNA1C:calcium voltage-gated channel subunit alpha1 C [Gene - OMIM - HGNC]
  • CCDC77:coiled-coil domain containing 77 [Gene - HGNC]
  • DCP1B:decapping mRNA 1B [Gene - OMIM - HGNC]
  • FOXM1:forkhead box M1 [Gene - OMIM - HGNC]
  • ITFG2:integrin alpha FG-GAP repeat containing 2 [Gene - OMIM - HGNC]
  • LRTM2:leucine rich repeats and transmembrane domains 2 [Gene - HGNC]
  • LINC02371:long intergenic non-protein coding RNA 2371 [Gene - HGNC]
  • LINC02417:long intergenic non-protein coding RNA 2417 [Gene - HGNC]
  • LINC02455:long intergenic non-protein coding RNA 2455 [Gene - HGNC]
  • LINC02827:long intergenic non-protein coding RNA 2827 [Gene - HGNC]
  • LINC00940:long intergenic non-protein coding RNA 940 [Gene - HGNC]
  • LINC00942:long intergenic non-protein coding RNA 942 [Gene - HGNC]
  • KDM5A:lysine demethylase 5A [Gene - OMIM - HGNC]
  • MIR3649:microRNA 3649 [Gene - HGNC]
  • NINJ2:ninjurin 2 [Gene - OMIM - HGNC]
  • NRIP2:nuclear receptor interacting protein 2 [Gene - HGNC]
  • PARP11:poly(ADP-ribose) polymerase family member 11 [Gene - OMIM - HGNC]
  • PRMT8:protein arginine methyltransferase 8 [Gene - OMIM - HGNC]
  • SLC6A12:solute carrier family 6 member 12 [Gene - OMIM - HGNC]
  • SLC6A13:solute carrier family 6 member 13 [Gene - OMIM - HGNC]
  • TEX52:testis expressed 52 [Gene - HGNC]
  • TSPAN9:tetraspanin 9 [Gene - OMIM - HGNC]
  • THCAT155:thyroid cancer-associated transcript 155 [Gene]
  • LOC100128253:uncharacterized LOC100128253 [Gene]
  • LOC102723544:uncharacterized LOC102723544 [Gene]
  • LOC105369595:uncharacterized LOC105369595 [Gene]
  • LOC107984507:uncharacterized LOC107984507 [Gene]
  • LOC574538:uncharacterized LOC574538 [Gene]
Variant type:
copy number loss
Cytogenetic location:
12p13.33-13.32
Genomic location:
Preferred name:
GRCh38/hg38 12p13.33-13.32(chr12:54427-4004912)x1
HGVS:
  • NC_000012.12:g.(?_54427)_(4004912_?)del
  • NC_000012.10:g.(?_33854)_(3984339_?)del
  • NC_000012.11:g.(?_282465)_(4114078_?)del
Links:
dbVar: nssv1608135; dbVar: nsv932370
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
SCV000181853ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Dec 3, 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, SCV000181853.4

#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