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GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)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:
RCV000053266.5

Allele description [Variation Report for GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1]

GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1

Genes:
  • ADGRL3-AS1:ADGRL3 antisense RNA 1 [Gene - HGNC]
  • ARL9:ADP ribosylation factor like GTPase 9 [Gene - OMIM - HGNC]
  • LOC129992610:ATAC-STARR-seq lymphoblastoid active region 21572 [Gene]
  • LOC129992611:ATAC-STARR-seq lymphoblastoid active region 21573 [Gene]
  • LOC129992614:ATAC-STARR-seq lymphoblastoid active region 21574 [Gene]
  • LOC129992620:ATAC-STARR-seq lymphoblastoid active region 21575 [Gene]
  • LOC129992621:ATAC-STARR-seq lymphoblastoid active region 21576 [Gene]
  • LOC129992622:ATAC-STARR-seq lymphoblastoid active region 21579 [Gene]
  • LOC129992625:ATAC-STARR-seq lymphoblastoid active region 21580 [Gene]
  • LOC129992629:ATAC-STARR-seq lymphoblastoid active region 21581 [Gene]
  • LOC129992630:ATAC-STARR-seq lymphoblastoid active region 21582 [Gene]
  • LOC129992631:ATAC-STARR-seq lymphoblastoid active region 21583 [Gene]
  • LOC129992632:ATAC-STARR-seq lymphoblastoid active region 21584 [Gene]
  • LOC129992635:ATAC-STARR-seq lymphoblastoid active region 21585 [Gene]
  • LOC129992637:ATAC-STARR-seq lymphoblastoid active region 21586 [Gene]
  • LOC129992639:ATAC-STARR-seq lymphoblastoid active region 21587 [Gene]
  • LOC129992640:ATAC-STARR-seq lymphoblastoid active region 21588 [Gene]
  • LOC129992612:ATAC-STARR-seq lymphoblastoid silent region 15438 [Gene]
  • LOC129992613:ATAC-STARR-seq lymphoblastoid silent region 15439 [Gene]
  • LOC129992615:ATAC-STARR-seq lymphoblastoid silent region 15440 [Gene]
  • LOC129992616:ATAC-STARR-seq lymphoblastoid silent region 15441 [Gene]
  • LOC129992617:ATAC-STARR-seq lymphoblastoid silent region 15442 [Gene]
  • LOC129992618:ATAC-STARR-seq lymphoblastoid silent region 15443 [Gene]
  • LOC129992619:ATAC-STARR-seq lymphoblastoid silent region 15445 [Gene]
  • LOC129992623:ATAC-STARR-seq lymphoblastoid silent region 15449 [Gene]
  • LOC129992624:ATAC-STARR-seq lymphoblastoid silent region 15450 [Gene]
  • LOC129992626:ATAC-STARR-seq lymphoblastoid silent region 15451 [Gene]
  • LOC129992627:ATAC-STARR-seq lymphoblastoid silent region 15452 [Gene]
  • LOC129992628:ATAC-STARR-seq lymphoblastoid silent region 15453 [Gene]
  • LOC129992633:ATAC-STARR-seq lymphoblastoid silent region 15454 [Gene]
  • LOC129992634:ATAC-STARR-seq lymphoblastoid silent region 15455 [Gene]
  • LOC129992636:ATAC-STARR-seq lymphoblastoid silent region 15457 [Gene]
  • LOC129992638:ATAC-STARR-seq lymphoblastoid silent region 15458 [Gene]
  • LOC129992641:ATAC-STARR-seq lymphoblastoid silent region 15459 [Gene]
  • LOC129992642:ATAC-STARR-seq lymphoblastoid silent region 15460 [Gene]
  • LOC126807054:BRD4-independent group 4 enhancer GRCh37_chr4:55147260-55148459 [Gene]
  • LOC126807055:BRD4-independent group 4 enhancer GRCh37_chr4:55878694-55879893 [Gene]
  • LOC126807063:BRD4-independent group 4 enhancer GRCh37_chr4:61589695-61590894 [Gene]
  • LOC126807057:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:56726227-56727426 [Gene]
  • LOC116158487:CRISPRi-validated cis-regulatory element chr4.1578 [Gene]
  • LOC116158488:CRISPRi-validated cis-regulatory element chr4.1581 [Gene]
  • LOC116158489:CRISPRi-validated cis-regulatory element chr4.1623 [Gene]
  • LOC116158490:CRISPRi-validated cis-regulatory element chr4.1625 [Gene]
  • LOC116158491:CRISPRi-validated cis-regulatory element chr4.1626 [Gene]
  • LOC116158492:CRISPRi-validated cis-regulatory element chr4.1627 [Gene]
  • LOC116158493:CRISPRi-validated cis-regulatory element chr4.1628 [Gene]
  • HOPX:HOP homeobox [Gene - OMIM - HGNC]
  • IGFBP7-AS1:IGFBP7 antisense RNA 1 [Gene - HGNC]
  • KIT:KIT proto-oncogene, receptor tyrosine kinase [Gene - OMIM - HGNC]
  • LOC126807056:MED14-independent group 3 enhancer GRCh37_chr4:56041662-56042861 [Gene]
  • LOC126807059:MED14-independent group 3 enhancer GRCh37_chr4:57176503-57177702 [Gene]
  • LOC126807060:MED14-independent group 3 enhancer GRCh37_chr4:57325164-57326363 [Gene]
  • LOC126807064:MED14-independent group 3 enhancer GRCh37_chr4:61799272-61800471 [Gene]
  • LOC126807058:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:56786864-56788063 [Gene]
  • LOC126807061:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:57506917-57508116 [Gene]
  • LOC126807062:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:57802865-57804064 [Gene]
  • REST:RE1 silencing transcription factor [Gene - OMIM - HGNC]
  • POLR2B:RNA polymerase II subunit B [Gene - OMIM - HGNC]
  • SRD5A3-AS1:SRD5A3 antisense RNA 1 [Gene - HGNC]
  • LOC121053182:Sharpr-MPRA regulatory region 11493 [Gene]
  • LOC121053179:Sharpr-MPRA regulatory region 12160 [Gene]
  • LOC123477745:Sharpr-MPRA regulatory region 15506 [Gene]
  • LOC123477748:Sharpr-MPRA regulatory region 1726 [Gene]
  • LOC123477744:Sharpr-MPRA regulatory region 1754 [Gene]
  • LOC121053181:Sharpr-MPRA regulatory region 1933 [Gene]
  • LOC121725171:Sharpr-MPRA regulatory region 5602 [Gene]
  • LOC123477746:Sharpr-MPRA regulatory region 6073 [Gene]
  • LOC121053180:Sharpr-MPRA regulatory region 7030 [Gene]
  • LOC123477747:Sharpr-MPRA regulatory region 7637 [Gene]
  • LOC123477743:Sharpr-MPRA regulatory region 7950 [Gene]
  • LOC123477749:Sharpr-MPRA regulatory region 909 [Gene]
  • LOC110121177:VISTA enhancer hs1651 [Gene]
  • ADGRL3:adhesion G protein-coupled receptor L3 [Gene - OMIM - HGNC]
  • AASDH:aminoadipate-semialdehyde dehydrogenase [Gene - OMIM - HGNC]
  • CRACD:capping protein inhibiting regulator of actin dynamics [Gene - OMIM - HGNC]
  • CEP135:centrosomal protein 135 [Gene - OMIM - HGNC]
  • CLOCK:clock circadian regulator [Gene - OMIM - HGNC]
  • EXOC1L:exocyst complex component 1 like [Gene - HGNC]
  • EXOC1:exocyst complex component 1 [Gene - OMIM - HGNC]
  • IGFBP7:insulin like growth factor binding protein 7 [Gene - OMIM - HGNC]
  • KDR:kinase insert domain receptor [Gene - OMIM - HGNC]
  • LINC02260:long intergenic non-protein coding RNA 2260 [Gene - HGNC]
  • LINC02271:long intergenic non-protein coding RNA 2271 [Gene - HGNC]
  • LINC02283:long intergenic non-protein coding RNA 2283 [Gene - HGNC]
  • LINC02380:long intergenic non-protein coding RNA 2380 [Gene - HGNC]
  • LINC02429:long intergenic non-protein coding RNA 2429 [Gene - HGNC]
  • LINC02494:long intergenic non-protein coding RNA 2494 [Gene - HGNC]
  • LINC02496:long intergenic non-protein coding RNA 2496 [Gene - HGNC]
  • LINC02619:long intergenic non-protein coding RNA 2619 [Gene - HGNC]
  • MIR548AG1:microRNA 548ag-1 [Gene - HGNC]
  • NMU:neuromedin U [Gene - OMIM - HGNC]
  • NOA1:nitric oxide associated 1 [Gene - OMIM - HGNC]
  • PDCL2:phosducin like 2 [Gene - OMIM - HGNC]
  • PPAT:phosphoribosyl pyrophosphate amidotransferase [Gene - OMIM - HGNC]
  • PAICS:phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase [Gene - OMIM - HGNC]
  • PDGFRA:platelet derived growth factor receptor alpha [Gene - OMIM - HGNC]
  • SPINK2:serine peptidase inhibitor Kazal type 2 [Gene - OMIM - HGNC]
  • SRP72:signal recognition particle 72 [Gene - OMIM - HGNC]
  • SPMAP2L:sperm microtubule associated protein 2 like [Gene - HGNC]
  • SRD5A3:steroid 5 alpha-reductase 3 [Gene - OMIM - HGNC]
  • TMEM165:transmembrane protein 165 [Gene - OMIM - HGNC]
  • LOC105377672:uncharacterized LOC105377672 [Gene]
Variant type:
copy number loss
Cytogenetic location:
4q12-13.1
Genomic location:
Preferred name:
GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1
HGVS:
  • NC_000004.12:g.(?_54198601)_(62270115_?)del
  • NC_000004.10:g.(?_54759525)_(62818428_?)del
  • NC_000004.11:g.(?_55064768)_(63135833_?)del
Links:
dbVar: nssv577973; dbVar: nsv531946
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
SCV000080624GeneDx
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, SCV000080624.4

#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