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GRCh38/hg38 12p13.2-12.3(chr12:12388842-15540422)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:
RCV000052780.5

Allele description [Variation Report for GRCh38/hg38 12p13.2-12.3(chr12:12388842-15540422)x1]

GRCh38/hg38 12p13.2-12.3(chr12:12388842-15540422)x1

Genes:
  • ART4:ADP-ribosyltransferase 4 (inactive) (Dombrock blood group) [Gene - OMIM - HGNC]
  • LOC130007439:ATAC-STARR-seq lymphoblastoid active region 6012 [Gene]
  • LOC130007440:ATAC-STARR-seq lymphoblastoid active region 6013 [Gene]
  • LOC130007445:ATAC-STARR-seq lymphoblastoid active region 6014 [Gene]
  • LOC130007447:ATAC-STARR-seq lymphoblastoid active region 6017 [Gene]
  • LOC130007448:ATAC-STARR-seq lymphoblastoid active region 6018 [Gene]
  • LOC130007449:ATAC-STARR-seq lymphoblastoid active region 6019 [Gene]
  • LOC130007450:ATAC-STARR-seq lymphoblastoid active region 6020 [Gene]
  • LOC130007451:ATAC-STARR-seq lymphoblastoid active region 6021 [Gene]
  • LOC130007452:ATAC-STARR-seq lymphoblastoid active region 6022 [Gene]
  • LOC130007453:ATAC-STARR-seq lymphoblastoid active region 6023 [Gene]
  • LOC130007454:ATAC-STARR-seq lymphoblastoid active region 6024 [Gene]
  • LOC130007455:ATAC-STARR-seq lymphoblastoid active region 6025 [Gene]
  • LOC130007457:ATAC-STARR-seq lymphoblastoid active region 6026 [Gene]
  • LOC130007458:ATAC-STARR-seq lymphoblastoid active region 6027 [Gene]
  • LOC130007459:ATAC-STARR-seq lymphoblastoid active region 6028 [Gene]
  • LOC130007460:ATAC-STARR-seq lymphoblastoid active region 6029 [Gene]
  • LOC130007466:ATAC-STARR-seq lymphoblastoid active region 6030 [Gene]
  • LOC130007469:ATAC-STARR-seq lymphoblastoid active region 6031 [Gene]
  • LOC130007475:ATAC-STARR-seq lymphoblastoid active region 6032 [Gene]
  • LOC130007476:ATAC-STARR-seq lymphoblastoid active region 6033 [Gene]
  • LOC130007477:ATAC-STARR-seq lymphoblastoid active region 6034 [Gene]
  • LOC130007478:ATAC-STARR-seq lymphoblastoid active region 6035 [Gene]
  • LOC130007479:ATAC-STARR-seq lymphoblastoid active region 6036 [Gene]
  • LOC130007480:ATAC-STARR-seq lymphoblastoid active region 6037 [Gene]
  • LOC130007481:ATAC-STARR-seq lymphoblastoid active region 6038 [Gene]
  • LOC130007482:ATAC-STARR-seq lymphoblastoid active region 6041 [Gene]
  • LOC130007483:ATAC-STARR-seq lymphoblastoid active region 6042 [Gene]
  • LOC130007484:ATAC-STARR-seq lymphoblastoid active region 6043 [Gene]
  • LOC130007485:ATAC-STARR-seq lymphoblastoid active region 6046 [Gene]
  • LOC130007486:ATAC-STARR-seq lymphoblastoid active region 6047 [Gene]
  • LOC130007487:ATAC-STARR-seq lymphoblastoid active region 6048 [Gene]
  • LOC130007488:ATAC-STARR-seq lymphoblastoid active region 6049 [Gene]
  • LOC130007490:ATAC-STARR-seq lymphoblastoid active region 6050 [Gene]
  • LOC130007491:ATAC-STARR-seq lymphoblastoid active region 6051 [Gene]
  • LOC130007493:ATAC-STARR-seq lymphoblastoid active region 6057 [Gene]
  • LOC130007494:ATAC-STARR-seq lymphoblastoid active region 6058 [Gene]
  • LOC130007495:ATAC-STARR-seq lymphoblastoid active region 6059 [Gene]
  • LOC130007496:ATAC-STARR-seq lymphoblastoid active region 6060 [Gene]
  • LOC130007497:ATAC-STARR-seq lymphoblastoid active region 6061 [Gene]
  • LOC130007498:ATAC-STARR-seq lymphoblastoid active region 6062 [Gene]
  • LOC130007499:ATAC-STARR-seq lymphoblastoid active region 6063 [Gene]
  • LOC130007500:ATAC-STARR-seq lymphoblastoid active region 6064 [Gene]
  • LOC130007501:ATAC-STARR-seq lymphoblastoid active region 6065 [Gene]
  • LOC130007503:ATAC-STARR-seq lymphoblastoid active region 6067 [Gene]
  • LOC130007438:ATAC-STARR-seq lymphoblastoid silent region 4254 [Gene]
  • LOC130007441:ATAC-STARR-seq lymphoblastoid silent region 4255 [Gene]
  • LOC130007442:ATAC-STARR-seq lymphoblastoid silent region 4256 [Gene]
  • LOC130007443:ATAC-STARR-seq lymphoblastoid silent region 4257 [Gene]
  • LOC130007444:ATAC-STARR-seq lymphoblastoid silent region 4258 [Gene]
  • LOC130007446:ATAC-STARR-seq lymphoblastoid silent region 4260 [Gene]
  • LOC130007456:ATAC-STARR-seq lymphoblastoid silent region 4261 [Gene]
  • LOC130007461:ATAC-STARR-seq lymphoblastoid silent region 4262 [Gene]
  • LOC130007462:ATAC-STARR-seq lymphoblastoid silent region 4263 [Gene]
  • LOC130007463:ATAC-STARR-seq lymphoblastoid silent region 4264 [Gene]
  • LOC130007464:ATAC-STARR-seq lymphoblastoid silent region 4265 [Gene]
  • LOC130007465:ATAC-STARR-seq lymphoblastoid silent region 4266 [Gene]
  • LOC130007467:ATAC-STARR-seq lymphoblastoid silent region 4267 [Gene]
  • LOC130007468:ATAC-STARR-seq lymphoblastoid silent region 4268 [Gene]
  • LOC130007470:ATAC-STARR-seq lymphoblastoid silent region 4269 [Gene]
  • LOC130007471:ATAC-STARR-seq lymphoblastoid silent region 4270 [Gene]
  • LOC130007472:ATAC-STARR-seq lymphoblastoid silent region 4271 [Gene]
  • LOC130007473:ATAC-STARR-seq lymphoblastoid silent region 4272 [Gene]
  • LOC130007474:ATAC-STARR-seq lymphoblastoid silent region 4273 [Gene]
  • LOC130007489:ATAC-STARR-seq lymphoblastoid silent region 4275 [Gene]
  • LOC130007492:ATAC-STARR-seq lymphoblastoid silent region 4276 [Gene]
  • LOC130007502:ATAC-STARR-seq lymphoblastoid silent region 4277 [Gene]
  • BORCS5:BLOC-1 related complex subunit 5 [Gene - OMIM - HGNC]
  • LOC126861454:BRD4-independent group 4 enhancer GRCh37_chr12:12796246-12797445 [Gene]
  • LOC126861456:BRD4-independent group 4 enhancer GRCh37_chr12:12975829-12977028 [Gene]
  • LOC112163543:BRD4-independent group 4 enhancer GRCh37_chr12:13318180-13319379 [Gene]
  • LOC126861466:BRD4-independent group 4 enhancer GRCh37_chr12:15103381-15104580 [Gene]
  • LOC126861459:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:13237538-13238737 [Gene]
  • LOC126861461:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:13528282-13529481 [Gene]
  • LOC126861463:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:14372961-14374160 [Gene]
  • LOC126861465:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:15033676-15034875 [Gene]
  • LOC126861467:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:15678492-15679691 [Gene]
  • LOC116268435:CRISPRi-validated cis-regulatory element chr12.662 [Gene]
  • DDX47:DEAD-box helicase 47 [Gene - OMIM - HGNC]
  • GPR19:G protein-coupled receptor 19 [Gene - OMIM - HGNC]
  • GPRC5A:G protein-coupled receptor class C group 5 member A [Gene - OMIM - HGNC]
  • GPRC5D:G protein-coupled receptor class C group 5 member D [Gene - OMIM - HGNC]
  • GPRC5D-AS1:GPRC5D and HEBP1 antisense RNA 1 [Gene - HGNC]
  • GUCY2C-AS1:GUCY2C antisense RNA 1 [Gene - HGNC]
  • H2AJ:H2A.J histone [Gene - HGNC]
  • H4C16:H4 histone 16 [Gene - OMIM - HGNC]
  • LOC121466692:MED14-independent group 3 enhancer GRCh37_chr12:12592110-12593309 [Gene]
  • LOC126861453:MED14-independent group 3 enhancer GRCh37_chr12:12753351-12754550 [Gene]
  • LOC126861457:MED14-independent group 3 enhancer GRCh37_chr12:12987821-12989020 [Gene]
  • LOC126861460:MED14-independent group 3 enhancer GRCh37_chr12:13492223-13493422 [Gene]
  • LOC126861464:MED14-independent group 3 enhancer GRCh37_chr12:14658416-14659615 [Gene]
  • LOC126861468:MED14-independent group 3 enhancer GRCh37_chr12:15687897-15689096 [Gene]
  • LOC129390401:MPRA-validated peak1575 silencer [Gene]
  • LOC129390402:MPRA-validated peak1577 silencer [Gene]
  • LOC129390403:MPRA-validated peak1579 silencer [Gene]
  • LOC132090038:Neanderthal introgressed variant-containing enhancer experimental_25257 [Gene]
  • LOC132090065:Neanderthal introgressed variant-containing enhancer experimental_26314 [Gene]
  • LOC126861455:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:12956863-12958062 [Gene]
  • LOC126861458:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:13024682-13025881 [Gene]
  • LOC126861462:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:14138289-14139488 [Gene]
  • PLBD1-AS1:PLBD1 antisense RNA 1 [Gene - HGNC]
  • RERG:RAS like estrogen regulated growth inhibitor [Gene - OMIM - HGNC]
  • RERG-AS1:RERG antisense RNA 1 [Gene - HGNC]
  • RERG-IT1:RERG intronic transcript 1 [Gene - HGNC]
  • LOC108281141:RPL13AP20-GPRC5A intergenic CAGE-defined mid-level expression enhancer [Gene]
  • ARHGDIB:Rho GDP dissociation inhibitor beta [Gene - OMIM - HGNC]
  • LOC112163545:Sharpr-MPRA regulatory region 1480 [Gene]
  • LOC124625911:Sharpr-MPRA regulatory region 1907 [Gene]
  • LOC124625909:Sharpr-MPRA regulatory region 2795 [Gene]
  • LOC112163544:Sharpr-MPRA regulatory region 3500 [Gene]
  • LOC124625913:Sharpr-MPRA regulatory region 453 [Gene]
  • LOC124625912:Sharpr-MPRA regulatory region 5402 [Gene]
  • LOC124625910:Sharpr-MPRA regulatory region 6445 [Gene]
  • LOC124625908:Sharpr-MPRA regulatory region 7135 [Gene]
  • WBP11:WW domain binding protein 11 [Gene - OMIM - HGNC]
  • ATF7IP:activating transcription factor 7 interacting protein [Gene - OMIM - HGNC]
  • APOLD1:apolipoprotein L domain containing 1 [Gene - OMIM - HGNC]
  • CREBL2:cAMP responsive element binding protein like 2 [Gene - OMIM - HGNC]
  • C12orf60:chromosome 12 open reading frame 60 [Gene - HGNC]
  • CDKN1B:cyclin dependent kinase inhibitor 1B [Gene - OMIM - HGNC]
  • DUSP16:dual specificity phosphatase 16 [Gene - OMIM - HGNC]
  • ERP27:endoplasmic reticulum protein 27 [Gene - OMIM - HGNC]
  • EMP1:epithelial membrane protein 1 [Gene - OMIM - HGNC]
  • FAM234B:family with sequence similarity 234 member B [Gene - OMIM - HGNC]
  • GSG1:germ cell associated 1 [Gene - HGNC]
  • GRIN2B:glutamate ionotropic receptor NMDA type subunit 2B [Gene - OMIM - HGNC]
  • GUCY2C:guanylate cyclase 2C [Gene - OMIM - HGNC]
  • HEBP1:heme binding protein 1 [Gene - OMIM - HGNC]
  • LINC01489:long intergenic non-protein coding RNA 1489 [Gene - HGNC]
  • LINC01559:long intergenic non-protein coding RNA 1559 [Gene - HGNC]
  • MGP:matrix Gla protein [Gene - OMIM - HGNC]
  • LOC128772374:melanoma risk locus-associated MPRA allelic enhancer 12:13058787 [Gene]
  • LOC128772375:melanoma risk locus-associated MPRA allelic enhancer 12:13059781 [Gene]
  • LOC128781585:melanoma risk locus-associated MPRA allelic enhancer 12:13073965 [Gene]
  • LOC128732306:melanoma risk locus-associated MPRA allelic enhancer 12:13075202 [Gene]
  • MIR613:microRNA 613 [Gene - HGNC]
  • MIR614:microRNA 614 [Gene - HGNC]
  • PDE6H:phosphodiesterase 6H [Gene - OMIM - HGNC]
  • PLBD1:phospholipase B domain containing 1 [Gene - OMIM - HGNC]
  • PTPRO:protein tyrosine phosphatase receptor type O [Gene - OMIM - HGNC]
  • SMCO3:single-pass membrane protein with coiled-coil domains 3 [Gene - HGNC]
  • LOC101928317:uncharacterized LOC101928317 [Gene]
Variant type:
copy number loss
Cytogenetic location:
12p13.2-12.3
Genomic location:
Preferred name:
GRCh38/hg38 12p13.2-12.3(chr12:12388842-15540422)x1
HGVS:
  • NC_000012.12:g.(?_12388842)_(15540422_?)del
  • NC_000012.10:g.(?_12433043)_(15584623_?)del
  • NC_000012.11:g.(?_12541776)_(15693356_?)del
Links:
dbVar: nssv577378; dbVar: nsv531497
Observations:
1

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000080134GeneDx
criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))
Pathogenic
(Aug 12, 2011)
de novoclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not 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 GeneDx, SCV000080134.4

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

Last Updated: Oct 14, 2023