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GRCh38/hg38 12p13.31(chr12:6728665-7705620)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:
RCV000052779.4

Allele description [Variation Report for GRCh38/hg38 12p13.31(chr12:6728665-7705620)x1]

GRCh38/hg38 12p13.31(chr12:6728665-7705620)x1

Genes:
  • LOC130007270:ATAC-STARR-seq lymphoblastoid active region 5879 [Gene]
  • LOC130007271:ATAC-STARR-seq lymphoblastoid active region 5880 [Gene]
  • LOC130007275:ATAC-STARR-seq lymphoblastoid active region 5883 [Gene]
  • LOC130007277:ATAC-STARR-seq lymphoblastoid active region 5885 [Gene]
  • LOC130007282:ATAC-STARR-seq lymphoblastoid active region 5888 [Gene]
  • LOC130007285:ATAC-STARR-seq lymphoblastoid active region 5889 [Gene]
  • LOC130007286:ATAC-STARR-seq lymphoblastoid active region 5890 [Gene]
  • LOC130007287:ATAC-STARR-seq lymphoblastoid active region 5891 [Gene]
  • LOC130007292:ATAC-STARR-seq lymphoblastoid active region 5896 [Gene]
  • LOC130007293:ATAC-STARR-seq lymphoblastoid active region 5897 [Gene]
  • LOC130007294:ATAC-STARR-seq lymphoblastoid active region 5898 [Gene]
  • LOC130007295:ATAC-STARR-seq lymphoblastoid active region 5899 [Gene]
  • LOC130007296:ATAC-STARR-seq lymphoblastoid active region 5900 [Gene]
  • LOC130007297:ATAC-STARR-seq lymphoblastoid active region 5901 [Gene]
  • LOC130007298:ATAC-STARR-seq lymphoblastoid active region 5902 [Gene]
  • LOC130007299:ATAC-STARR-seq lymphoblastoid active region 5903 [Gene]
  • LOC130007300:ATAC-STARR-seq lymphoblastoid active region 5904 [Gene]
  • LOC130007301:ATAC-STARR-seq lymphoblastoid active region 5905 [Gene]
  • LOC130007302:ATAC-STARR-seq lymphoblastoid active region 5906 [Gene]
  • LOC130007303:ATAC-STARR-seq lymphoblastoid active region 5907 [Gene]
  • LOC130007304:ATAC-STARR-seq lymphoblastoid active region 5908 [Gene]
  • LOC130007305:ATAC-STARR-seq lymphoblastoid active region 5910 [Gene]
  • LOC130007309:ATAC-STARR-seq lymphoblastoid active region 5916 [Gene]
  • LOC130007312:ATAC-STARR-seq lymphoblastoid active region 5919 [Gene]
  • LOC130007269:ATAC-STARR-seq lymphoblastoid silent region 4179 [Gene]
  • LOC130007272:ATAC-STARR-seq lymphoblastoid silent region 4180 [Gene]
  • LOC130007273:ATAC-STARR-seq lymphoblastoid silent region 4181 [Gene]
  • LOC130007274:ATAC-STARR-seq lymphoblastoid silent region 4182 [Gene]
  • LOC130007276:ATAC-STARR-seq lymphoblastoid silent region 4184 [Gene]
  • LOC130007278:ATAC-STARR-seq lymphoblastoid silent region 4186 [Gene]
  • LOC130007279:ATAC-STARR-seq lymphoblastoid silent region 4187 [Gene]
  • LOC130007280:ATAC-STARR-seq lymphoblastoid silent region 4188 [Gene]
  • LOC130007281:ATAC-STARR-seq lymphoblastoid silent region 4189 [Gene]
  • LOC130007283:ATAC-STARR-seq lymphoblastoid silent region 4190 [Gene]
  • LOC130007284:ATAC-STARR-seq lymphoblastoid silent region 4191 [Gene]
  • LOC130007288:ATAC-STARR-seq lymphoblastoid silent region 4193 [Gene]
  • LOC130007289:ATAC-STARR-seq lymphoblastoid silent region 4194 [Gene]
  • LOC130007290:ATAC-STARR-seq lymphoblastoid silent region 4195 [Gene]
  • LOC130007291:ATAC-STARR-seq lymphoblastoid silent region 4196 [Gene]
  • LOC130007306:ATAC-STARR-seq lymphoblastoid silent region 4197 [Gene]
  • LOC130007307:ATAC-STARR-seq lymphoblastoid silent region 4198 [Gene]
  • LOC130007308:ATAC-STARR-seq lymphoblastoid silent region 4199 [Gene]
  • LOC130007310:ATAC-STARR-seq lymphoblastoid silent region 4202 [Gene]
  • LOC130007311:ATAC-STARR-seq lymphoblastoid silent region 4203 [Gene]
  • LOC126861435:BRD4-independent group 4 enhancer GRCh37_chr12:7476238-7477437 [Gene]
  • C1RL-AS1:C1RL antisense RNA 1 [Gene - HGNC]
  • CD163L1:CD163 molecule like 1 [Gene - OMIM - HGNC]
  • CD163:CD163 molecule [Gene - OMIM - HGNC]
  • CD4:CD4 molecule [Gene - OMIM - HGNC]
  • COPS7A:COP9 signalosome subunit 7A [Gene - OMIM - HGNC]
  • EMG1:EMG1 N1-specific pseudouridine methyltransferase [Gene - OMIM - HGNC]
  • GNB3:G protein subunit beta 3 [Gene - OMIM - HGNC]
  • GPR162:G protein-coupled receptor 162 [Gene - HGNC]
  • LOC126861433:MED14-independent group 3 enhancer GRCh37_chr12:7260830-7262029 [Gene]
  • LOC126861434:MED14-independent group 3 enhancer GRCh37_chr12:7469109-7470308 [Gene]
  • MIR200CHG:MIR200C and MIR141 host gene [Gene - HGNC]
  • LOC129390390:MPRA-validated peak1553 silencer [Gene]
  • LOC129390391:MPRA-validated peak1554 silencer [Gene]
  • LOC129390392:MPRA-validated peak1556 silencer [Gene]
  • LOC129390393:MPRA-validated peak1559 silencer [Gene]
  • LOC132090142:Neanderthal introgressed variant-containing enhancer experimental_30893 [Gene]
  • LOC126861436:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:7521391-7522590 [Gene]
  • LOC126861437:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:7736568-7737767 [Gene]
  • RNU7-1:RNA, U7 small nuclear 1 [Gene - OMIM - HGNC]
  • LOC112163630:Sharpr-MPRA regulatory region 10898 [Gene]
  • LOC124625896:Sharpr-MPRA regulatory region 1171 [Gene]
  • LOC121466690:Sharpr-MPRA regulatory region 13430 [Gene]
  • LOC121466689:Sharpr-MPRA regulatory region 13442 [Gene]
  • LOC124625897:Sharpr-MPRA regulatory region 5519 [Gene]
  • ACSM4:acyl-CoA synthetase medium chain family member 4 [Gene - OMIM - HGNC]
  • APOBEC1:apolipoprotein B mRNA editing enzyme catalytic subunit 1 [Gene - OMIM - HGNC]
  • LOC109461484:atrophin 1 repeat instability region [Gene]
  • ATN1:atrophin 1 [Gene - OMIM - HGNC]
  • CLSTN3:calsyntenin 3 [Gene - OMIM - HGNC]
  • CDCA3:cell division cycle associated 3 [Gene - OMIM - HGNC]
  • C12orf57:chromosome 12 open reading frame 57 [Gene - OMIM - HGNC]
  • C1RL:complement C1r subcomponent like [Gene - OMIM - HGNC]
  • C1R:complement C1r [Gene - OMIM - HGNC]
  • C1S:complement C1s [Gene - OMIM - HGNC]
  • ENO2:enolase 2 [Gene - OMIM - HGNC]
  • GDF3:growth differentiation factor 3 [Gene - OMIM - HGNC]
  • LRRC23:leucine rich repeat containing 23 [Gene - HGNC]
  • LAG3:lymphocyte activating 3 [Gene - OMIM - HGNC]
  • LPCAT3:lysophosphatidylcholine acyltransferase 3 [Gene - OMIM - HGNC]
  • MIR141:microRNA 141 [Gene - OMIM - HGNC]
  • MIR200C:microRNA 200c [Gene - OMIM - HGNC]
  • MLF2:myeloid leukemia factor 2 [Gene - OMIM - HGNC]
  • LOC106799839:nonconserved acetylation island sequence 91 enhancer [Gene]
  • PTMS:parathymosin [Gene - OMIM - HGNC]
  • PEX5:peroxisomal biogenesis factor 5 [Gene - OMIM - HGNC]
  • PHB2:prohibitin 2 [Gene - OMIM - HGNC]
  • P3H3:prolyl 3-hydroxylase 3 [Gene - OMIM - HGNC]
  • PTPN6:protein tyrosine phosphatase non-receptor type 6 [Gene - OMIM - HGNC]
  • RBP5:retinol binding protein 5 [Gene - OMIM - HGNC]
  • SCARNA12:small Cajal body-specific RNA 12 [Gene - OMIM - HGNC]
  • SPSB2:splA/ryanodine receptor domain and SOCS box containing 2 [Gene - OMIM - HGNC]
  • TPI1:triosephosphate isomerase 1 [Gene - OMIM - HGNC]
  • USP5:ubiquitin specific peptidase 5 [Gene - OMIM - HGNC]
  • LOC105369632:uncharacterized LOC105369632 [Gene]
Variant type:
copy number loss
Cytogenetic location:
12p13.31
Genomic location:
Preferred name:
GRCh38/hg38 12p13.31(chr12:6728665-7705620)x1
HGVS:
  • NC_000012.12:g.(?_6728665)_(7705620_?)del
  • NC_000012.10:g.(?_6708092)_(7749483_?)del
  • NC_000012.11:g.(?_6837831)_(7858216_?)del
Links:
dbVar: nssv577376; dbVar: nsv531496
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
SCV000080133GeneDx
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 GeneDx, SCV000080133.4

#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