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GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)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:
RCV000052813.5

Allele description

GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1

Genes:
  • AGAP2-AS1:AGAP2 antisense RNA 1 [Gene - HGNC]
  • LOC130008108:ATAC-STARR-seq lymphoblastoid active region 6520 [Gene]
  • LOC130008109:ATAC-STARR-seq lymphoblastoid active region 6521 [Gene]
  • LOC130008110:ATAC-STARR-seq lymphoblastoid active region 6522 [Gene]
  • LOC130008111:ATAC-STARR-seq lymphoblastoid active region 6523 [Gene]
  • LOC130008112:ATAC-STARR-seq lymphoblastoid active region 6524 [Gene]
  • LOC130008115:ATAC-STARR-seq lymphoblastoid active region 6525 [Gene]
  • LOC130008120:ATAC-STARR-seq lymphoblastoid active region 6527 [Gene]
  • LOC130008124:ATAC-STARR-seq lymphoblastoid active region 6528 [Gene]
  • LOC130008125:ATAC-STARR-seq lymphoblastoid active region 6529 [Gene]
  • LOC130008126:ATAC-STARR-seq lymphoblastoid active region 6530 [Gene]
  • LOC130008127:ATAC-STARR-seq lymphoblastoid active region 6532 [Gene]
  • LOC130008129:ATAC-STARR-seq lymphoblastoid active region 6534 [Gene]
  • LOC130008130:ATAC-STARR-seq lymphoblastoid active region 6535 [Gene]
  • LOC130008132:ATAC-STARR-seq lymphoblastoid active region 6536 [Gene]
  • LOC130008133:ATAC-STARR-seq lymphoblastoid active region 6537 [Gene]
  • LOC130008135:ATAC-STARR-seq lymphoblastoid active region 6538 [Gene]
  • LOC130008136:ATAC-STARR-seq lymphoblastoid active region 6539 [Gene]
  • LOC130008137:ATAC-STARR-seq lymphoblastoid active region 6540 [Gene]
  • LOC130008138:ATAC-STARR-seq lymphoblastoid active region 6541 [Gene]
  • LOC130008139:ATAC-STARR-seq lymphoblastoid active region 6542 [Gene]
  • LOC130008140:ATAC-STARR-seq lymphoblastoid active region 6548 [Gene]
  • LOC130008142:ATAC-STARR-seq lymphoblastoid active region 6549 [Gene]
  • LOC130008144:ATAC-STARR-seq lymphoblastoid active region 6550 [Gene]
  • LOC130008145:ATAC-STARR-seq lymphoblastoid active region 6551 [Gene]
  • LOC130008146:ATAC-STARR-seq lymphoblastoid active region 6552 [Gene]
  • LOC130008147:ATAC-STARR-seq lymphoblastoid active region 6553 [Gene]
  • LOC130008152:ATAC-STARR-seq lymphoblastoid active region 6554 [Gene]
  • LOC130008153:ATAC-STARR-seq lymphoblastoid active region 6555 [Gene]
  • LOC130008154:ATAC-STARR-seq lymphoblastoid active region 6556 [Gene]
  • LOC130008155:ATAC-STARR-seq lymphoblastoid active region 6560 [Gene]
  • LOC130008156:ATAC-STARR-seq lymphoblastoid active region 6561 [Gene]
  • LOC130008163:ATAC-STARR-seq lymphoblastoid active region 6564 [Gene]
  • LOC130008164:ATAC-STARR-seq lymphoblastoid active region 6565 [Gene]
  • LOC130008165:ATAC-STARR-seq lymphoblastoid active region 6566 [Gene]
  • LOC130008166:ATAC-STARR-seq lymphoblastoid active region 6567 [Gene]
  • LOC130008167:ATAC-STARR-seq lymphoblastoid active region 6568 [Gene]
  • LOC130008168:ATAC-STARR-seq lymphoblastoid active region 6569 [Gene]
  • LOC130008169:ATAC-STARR-seq lymphoblastoid active region 6570 [Gene]
  • LOC130008173:ATAC-STARR-seq lymphoblastoid active region 6571 [Gene]
  • LOC130008174:ATAC-STARR-seq lymphoblastoid active region 6572 [Gene]
  • LOC130008175:ATAC-STARR-seq lymphoblastoid active region 6573 [Gene]
  • LOC130008177:ATAC-STARR-seq lymphoblastoid active region 6574 [Gene]
  • LOC130008178:ATAC-STARR-seq lymphoblastoid active region 6575 [Gene]
  • LOC130008179:ATAC-STARR-seq lymphoblastoid active region 6576 [Gene]
  • LOC130008182:ATAC-STARR-seq lymphoblastoid active region 6577 [Gene]
  • LOC130008183:ATAC-STARR-seq lymphoblastoid active region 6578 [Gene]
  • LOC130008184:ATAC-STARR-seq lymphoblastoid active region 6579 [Gene]
  • LOC130008185:ATAC-STARR-seq lymphoblastoid active region 6580 [Gene]
  • LOC130008188:ATAC-STARR-seq lymphoblastoid active region 6581 [Gene]
  • LOC130008189:ATAC-STARR-seq lymphoblastoid active region 6584 [Gene]
  • LOC130008113:ATAC-STARR-seq lymphoblastoid silent region 4569 [Gene]
  • LOC130008114:ATAC-STARR-seq lymphoblastoid silent region 4570 [Gene]
  • LOC130008116:ATAC-STARR-seq lymphoblastoid silent region 4571 [Gene]
  • LOC130008117:ATAC-STARR-seq lymphoblastoid silent region 4572 [Gene]
  • LOC130008118:ATAC-STARR-seq lymphoblastoid silent region 4573 [Gene]
  • LOC130008119:ATAC-STARR-seq lymphoblastoid silent region 4574 [Gene]
  • LOC130008121:ATAC-STARR-seq lymphoblastoid silent region 4575 [Gene]
  • LOC130008122:ATAC-STARR-seq lymphoblastoid silent region 4576 [Gene]
  • LOC130008123:ATAC-STARR-seq lymphoblastoid silent region 4578 [Gene]
  • LOC130008128:ATAC-STARR-seq lymphoblastoid silent region 4579 [Gene]
  • LOC130008131:ATAC-STARR-seq lymphoblastoid silent region 4580 [Gene]
  • LOC130008134:ATAC-STARR-seq lymphoblastoid silent region 4581 [Gene]
  • LOC130008141:ATAC-STARR-seq lymphoblastoid silent region 4584 [Gene]
  • LOC130008143:ATAC-STARR-seq lymphoblastoid silent region 4586 [Gene]
  • LOC130008148:ATAC-STARR-seq lymphoblastoid silent region 4588 [Gene]
  • LOC130008149:ATAC-STARR-seq lymphoblastoid silent region 4591 [Gene]
  • LOC130008150:ATAC-STARR-seq lymphoblastoid silent region 4592 [Gene]
  • LOC130008151:ATAC-STARR-seq lymphoblastoid silent region 4593 [Gene]
  • LOC130008157:ATAC-STARR-seq lymphoblastoid silent region 4594 [Gene]
  • LOC130008158:ATAC-STARR-seq lymphoblastoid silent region 4595 [Gene]
  • LOC130008159:ATAC-STARR-seq lymphoblastoid silent region 4596 [Gene]
  • LOC130008160:ATAC-STARR-seq lymphoblastoid silent region 4597 [Gene]
  • LOC130008161:ATAC-STARR-seq lymphoblastoid silent region 4598 [Gene]
  • LOC130008162:ATAC-STARR-seq lymphoblastoid silent region 4599 [Gene]
  • LOC130008170:ATAC-STARR-seq lymphoblastoid silent region 4600 [Gene]
  • LOC130008171:ATAC-STARR-seq lymphoblastoid silent region 4601 [Gene]
  • LOC130008172:ATAC-STARR-seq lymphoblastoid silent region 4602 [Gene]
  • LOC130008176:ATAC-STARR-seq lymphoblastoid silent region 4603 [Gene]
  • LOC130008180:ATAC-STARR-seq lymphoblastoid silent region 4604 [Gene]
  • LOC130008181:ATAC-STARR-seq lymphoblastoid silent region 4605 [Gene]
  • LOC130008186:ATAC-STARR-seq lymphoblastoid silent region 4606 [Gene]
  • LOC130008187:ATAC-STARR-seq lymphoblastoid silent region 4607 [Gene]
  • LOC130008190:ATAC-STARR-seq lymphoblastoid silent region 4610 [Gene]
  • LOC130008191:ATAC-STARR-seq lymphoblastoid silent region 4611 [Gene]
  • ATP23:ATP23 metallopeptidase and ATP synthase assembly factor homolog [Gene - OMIM - HGNC]
  • AGAP2:ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 [Gene - OMIM - HGNC]
  • LOC126861538:BRD4-independent group 4 enhancer GRCh37_chr12:57440635-57441834 [Gene]
  • LOC126861541:BRD4-independent group 4 enhancer GRCh37_chr12:57914069-57915268 [Gene]
  • LOC126861544:BRD4-independent group 4 enhancer GRCh37_chr12:58486590-58487789 [Gene]
  • LOC126861545:BRD4-independent group 4 enhancer GRCh37_chr12:58566454-58567653 [Gene]
  • LOC126861546:BRD4-independent group 4 enhancer GRCh37_chr12:58855785-58856984 [Gene]
  • LOC126861547:BRD4-independent group 4 enhancer GRCh37_chr12:59281329-59282528 [Gene]
  • LOC126861539:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:57570347-57571546 [Gene]
  • LOC126861540:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:57673563-57674762 [Gene]
  • LOC126861542:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:58127413-58128612 [Gene]
  • LOC126861543:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:58164747-58165946 [Gene]
  • CTDSP2:CTD small phosphatase 2 [Gene - OMIM - HGNC]
  • DDIT3:DNA damage inducible transcript 3 [Gene - OMIM - HGNC]
  • EEF1AKMT3:EEF1A lysine methyltransferase 3 [Gene - OMIM - HGNC]
  • GIHCG:GIHCG inhibitor of miR-200b/200a/429 expression [Gene - HGNC]
  • GLI1:GLI family zinc finger 1 [Gene - OMIM - HGNC]
  • LRP1:LDL receptor related protein 1 [Gene - OMIM - HGNC]
  • LRIG3-DT:LRIG3 divergent transcript [Gene - HGNC]
  • LRP1-AS:LRP1 antisense RNA [Gene - HGNC]
  • LOC126861548:MED14-independent group 3 enhancer GRCh37_chr12:59448831-59450030 [Gene]
  • LOC126861550:MED14-independent group 3 enhancer GRCh37_chr12:59751164-59752363 [Gene]
  • LOC126861552:MED14-independent group 3 enhancer GRCh37_chr12:62093041-62094240 [Gene]
  • LOC126861553:MED14-independent group 3 enhancer GRCh37_chr12:63118179-63119378 [Gene]
  • MIRLET7IHG:MIRLET7I host gene [Gene - HGNC]
  • MON2-AS1:MON2 antisense RNA 1 [Gene - HGNC]
  • MON2:MON2 homolog, regulator of endosome-to-Golgi trafficking [Gene - OMIM - HGNC]
  • LOC129390466:MPRA-validated peak1746 silencer [Gene]
  • LOC129390467:MPRA-validated peak1750 silencer [Gene]
  • LOC129390468:MPRA-validated peak1753 silencer [Gene]
  • NDUFA4L2:NDUFA4 mitochondrial complex associated like 2 [Gene - HGNC]
  • NAB2:NGFI-A binding protein 2 [Gene - OMIM - HGNC]
  • LOC132090129:Neanderthal introgressed variant-containing enhancer experimental_29738 [Gene]
  • LOC132090130:Neanderthal introgressed variant-containing enhancer experimental_29909 [Gene]
  • LOC132090131:Neanderthal introgressed variant-containing enhancer experimental_29986 [Gene]
  • LOC132090132:Neanderthal introgressed variant-containing enhancer experimental_30091 [Gene]
  • LOC132090133:Neanderthal introgressed variant-containing enhancer experimental_30105 [Gene]
  • LOC132090134:Neanderthal introgressed variant-containing enhancer experimental_30204 [Gene]
  • LOC132090135:Neanderthal introgressed variant-containing enhancer experimental_30226 [Gene]
  • LOC132090136:Neanderthal introgressed variant-containing enhancer experimental_30249 [Gene]
  • LOC132090137:Neanderthal introgressed variant-containing enhancer experimental_30360 [Gene]
  • LOC132090138:Neanderthal introgressed variant-containing enhancer experimental_30646 [Gene]
  • LOC132090139:Neanderthal introgressed variant-containing enhancer experimental_30791 [Gene]
  • OS9:OS9 endoplasmic reticulum lectin [Gene - OMIM - HGNC]
  • LOC126861549:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:59587037-59588236 [Gene]
  • LOC126861551:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:61045109-61046308 [Gene]
  • R3HDM2:R3H domain containing 2 [Gene - OMIM - HGNC]
  • R3HDM2-DT:R3HDM2 divergent transcript [Gene - HGNC]
  • ARHGAP9:Rho GTPase activating protein 9 [Gene - OMIM - HGNC]
  • ARHGEF25:Rho guanine nucleotide exchange factor 25 [Gene - OMIM - HGNC]
  • STAC3:SH3 and cysteine rich domain 3 [Gene - OMIM - HGNC]
  • LOC121466705:Sharpr-MPRA regulatory region 11134 [Gene]
  • LOC121832837:Sharpr-MPRA regulatory region 11351 [Gene]
  • LOC124629378:Sharpr-MPRA regulatory region 11633 [Gene]
  • LOC124629379:Sharpr-MPRA regulatory region 12928 [Gene]
  • LOC112163629:Sharpr-MPRA regulatory region 14116 [Gene]
  • LOC121832838:Sharpr-MPRA regulatory region 14680 [Gene]
  • LOC121832839:Sharpr-MPRA regulatory region 14765 [Gene]
  • LOC112163619:Sharpr-MPRA regulatory region 15392 [Gene]
  • LOC124629389:Sharpr-MPRA regulatory region 15489 [Gene]
  • LOC112163617:Sharpr-MPRA regulatory region 225 [Gene]
  • LOC124629388:Sharpr-MPRA regulatory region 3206 [Gene]
  • LOC112163628:Sharpr-MPRA regulatory region 3321 [Gene]
  • LOC112163618:Sharpr-MPRA regulatory region 358 [Gene]
  • LOC112163615:Sharpr-MPRA regulatory region 4597 [Gene]
  • LOC121466704:Sharpr-MPRA regulatory region 5413 [Gene]
  • LOC124629377:Sharpr-MPRA regulatory region 7317 [Gene]
  • LOC124629390:Sharpr-MPRA regulatory region 8347 [Gene]
  • LOC124629386:Sharpr-MPRA regulatory region 8919 [Gene]
  • LOC121466703:Sharpr-MPRA regulatory region 9665 [Gene]
  • TAFA2:TAFA chemokine like family member 2 [Gene - OMIM - HGNC]
  • TSFM:Ts translation elongation factor, mitochondrial [Gene - OMIM - HGNC]
  • LOC110121363:VISTA enhancer hs1427 [Gene]
  • LOC110121374:VISTA enhancer hs1468 [Gene]
  • AVIL:advillin [Gene - OMIM - HGNC]
  • B4GALNT1:beta-1,4-N-acetyl-galactosaminyltransferase 1 [Gene - OMIM - HGNC]
  • CDK4:cyclin dependent kinase 4 [Gene - OMIM - HGNC]
  • CYP27B1:cytochrome P450 family 27 subfamily B member 1 [Gene - OMIM - HGNC]
  • DTX3:deltex E3 ubiquitin ligase 3 [Gene - OMIM - HGNC]
  • DCTN2:dynactin subunit 2 [Gene - OMIM - HGNC]
  • INHBC:inhibin subunit beta C [Gene - OMIM - HGNC]
  • INHBE:inhibin subunit beta E [Gene - OMIM - HGNC]
  • KIF5A:kinesin family member 5A [Gene - OMIM - HGNC]
  • LRIG3:leucine rich repeats and immunoglobulin like domains 3 [Gene - OMIM - HGNC]
  • LINC01465:long intergenic non-protein coding RNA 1465 [Gene - HGNC]
  • LINC02388:long intergenic non-protein coding RNA 2388 [Gene - HGNC]
  • LINC02403:long intergenic non-protein coding RNA 2403 [Gene - HGNC]
  • LINC02448:long intergenic non-protein coding RNA 2448 [Gene - HGNC]
  • MARCHF9:membrane associated ring-CH-type finger 9 [Gene - OMIM - HGNC]
  • MARS1:methionyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
  • MBD6:methyl-CpG binding domain protein 6 [Gene - OMIM - HGNC]
  • METTL1:methyltransferase 1, tRNA methylguanosine [Gene - OMIM - HGNC]
  • MIR1228:microRNA 1228 [Gene - HGNC]
  • MIR26A2:microRNA 26a-2 [Gene - OMIM - HGNC]
  • MIR6125:microRNA 6125 [Gene - HGNC]
  • MIR616:microRNA 616 [Gene - OMIM - HGNC]
  • MIR6758:microRNA 6758 [Gene - HGNC]
  • MIR6759:microRNA 6759 [Gene - HGNC]
  • MIRLET7I:microRNA let-7i [Gene - OMIM - HGNC]
  • MYO1A:myosin IA [Gene - OMIM - HGNC]
  • NXPH4:neurexophilin 4 [Gene - OMIM - HGNC]
  • NEMP1:nuclear envelope integral membrane protein 1 [Gene - OMIM - HGNC]
  • PIP4K2C:phosphatidylinositol-5-phosphate 4-kinase type 2 gamma [Gene - OMIM - HGNC]
  • PPM1H:protein phosphatase, Mg2+/Mn2+ dependent 1H [Gene - OMIM - HGNC]
  • SHMT2:serine hydroxymethyltransferase 2 [Gene - OMIM - HGNC]
  • STAT6:signal transducer and activator of transcription 6 [Gene - OMIM - HGNC]
  • SLC16A7:solute carrier family 16 member 7 [Gene - OMIM - HGNC]
  • TAC3:tachykinin precursor 3 [Gene - OMIM - HGNC]
  • TSPAN31:tetraspanin 31 [Gene - OMIM - HGNC]
  • USP15:ubiquitin specific peptidase 15 [Gene - OMIM - HGNC]
  • LOC100506869:uncharacterized LOC100506869 [Gene]
  • LOC101927583:uncharacterized LOC101927583 [Gene]
  • LOC101927608:uncharacterized LOC101927608 [Gene]
  • LOC105369783:uncharacterized LOC105369783 [Gene]
  • LOC128125814:uncharacterized LOC128125814 [Gene]
  • LOC283387:uncharacterized LOC283387 [Gene]
Variant type:
copy number loss
Cytogenetic location:
12q13.3-14.2
Genomic location:
Preferred name:
GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1
HGVS:
  • NC_000012.12:g.(?_57013355)_(63042498_?)del
  • NC_000012.10:g.(?_55693406)_(61722545_?)del
  • NC_000012.11:g.(?_57407139)_(63436278_?)del
Links:
dbVar: nssv577388; dbVar: nsv531530
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
SCV000080167ISCA site 15

See additional submitters

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]

Help

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 ISCA site 15, SCV000080167.4

#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