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GRCh38/hg38 5q35.3(chr5:179669736-180897169)x1 AND See cases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 30, 2010
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:
RCV000135285.3

Allele description [Variation Report for GRCh38/hg38 5q35.3(chr5:179669736-180897169)x1]

GRCh38/hg38 5q35.3(chr5:179669736-180897169)x1

Genes:
  • LOC129995435:ATAC-STARR-seq lymphoblastoid active region 23756 [Gene]
  • LOC129995438:ATAC-STARR-seq lymphoblastoid active region 23757 [Gene]
  • LOC129995439:ATAC-STARR-seq lymphoblastoid active region 23758 [Gene]
  • LOC129995441:ATAC-STARR-seq lymphoblastoid active region 23759 [Gene]
  • LOC129995451:ATAC-STARR-seq lymphoblastoid active region 23765 [Gene]
  • LOC129995453:ATAC-STARR-seq lymphoblastoid active region 23766 [Gene]
  • LOC129995457:ATAC-STARR-seq lymphoblastoid active region 23767 [Gene]
  • LOC129995465:ATAC-STARR-seq lymphoblastoid active region 23768 [Gene]
  • LOC129995470:ATAC-STARR-seq lymphoblastoid active region 23769 [Gene]
  • LOC129995471:ATAC-STARR-seq lymphoblastoid active region 23770 [Gene]
  • LOC129995474:ATAC-STARR-seq lymphoblastoid active region 23771 [Gene]
  • LOC129995478:ATAC-STARR-seq lymphoblastoid active region 23772 [Gene]
  • LOC129995479:ATAC-STARR-seq lymphoblastoid active region 23773 [Gene]
  • LOC129995436:ATAC-STARR-seq lymphoblastoid silent region 16731 [Gene]
  • LOC129995437:ATAC-STARR-seq lymphoblastoid silent region 16732 [Gene]
  • LOC129995440:ATAC-STARR-seq lymphoblastoid silent region 16733 [Gene]
  • LOC129995442:ATAC-STARR-seq lymphoblastoid silent region 16735 [Gene]
  • LOC129995443:ATAC-STARR-seq lymphoblastoid silent region 16737 [Gene]
  • LOC129995444:ATAC-STARR-seq lymphoblastoid silent region 16739 [Gene]
  • LOC129995445:ATAC-STARR-seq lymphoblastoid silent region 16743 [Gene]
  • LOC129995446:ATAC-STARR-seq lymphoblastoid silent region 16744 [Gene]
  • LOC129995447:ATAC-STARR-seq lymphoblastoid silent region 16745 [Gene]
  • LOC129995448:ATAC-STARR-seq lymphoblastoid silent region 16746 [Gene]
  • LOC129995449:ATAC-STARR-seq lymphoblastoid silent region 16749 [Gene]
  • LOC129995450:ATAC-STARR-seq lymphoblastoid silent region 16750 [Gene]
  • LOC129995452:ATAC-STARR-seq lymphoblastoid silent region 16751 [Gene]
  • LOC129995454:ATAC-STARR-seq lymphoblastoid silent region 16752 [Gene]
  • LOC129995455:ATAC-STARR-seq lymphoblastoid silent region 16755 [Gene]
  • LOC129995456:ATAC-STARR-seq lymphoblastoid silent region 16756 [Gene]
  • LOC129995458:ATAC-STARR-seq lymphoblastoid silent region 16758 [Gene]
  • LOC129995459:ATAC-STARR-seq lymphoblastoid silent region 16759 [Gene]
  • LOC129995460:ATAC-STARR-seq lymphoblastoid silent region 16760 [Gene]
  • LOC129995461:ATAC-STARR-seq lymphoblastoid silent region 16761 [Gene]
  • LOC129995462:ATAC-STARR-seq lymphoblastoid silent region 16762 [Gene]
  • LOC129995463:ATAC-STARR-seq lymphoblastoid silent region 16763 [Gene]
  • LOC129995464:ATAC-STARR-seq lymphoblastoid silent region 16765 [Gene]
  • LOC129995466:ATAC-STARR-seq lymphoblastoid silent region 16766 [Gene]
  • LOC129995467:ATAC-STARR-seq lymphoblastoid silent region 16767 [Gene]
  • LOC129995468:ATAC-STARR-seq lymphoblastoid silent region 16768 [Gene]
  • LOC129995469:ATAC-STARR-seq lymphoblastoid silent region 16769 [Gene]
  • LOC129995472:ATAC-STARR-seq lymphoblastoid silent region 16773 [Gene]
  • LOC129995473:ATAC-STARR-seq lymphoblastoid silent region 16774 [Gene]
  • LOC129995475:ATAC-STARR-seq lymphoblastoid silent region 16775 [Gene]
  • LOC129995476:ATAC-STARR-seq lymphoblastoid silent region 16776 [Gene]
  • LOC129995477:ATAC-STARR-seq lymphoblastoid silent region 16777 [Gene]
  • LOC126807631:BRD4-independent group 4 enhancer GRCh37_chr5:179912532-179913731 [Gene]
  • CNOT6:CCR4-NOT transcription complex subunit 6 [Gene - OMIM - HGNC]
  • LOC126807627:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:179302124-179303323 [Gene]
  • LOC126807630:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:179894063-179895262 [Gene]
  • LOC126807632:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:180046831-180048030 [Gene]
  • LOC111556140:GATA motif-containing MPRA enhancer 81 [Gene]
  • LOC126807628:MED14-independent group 3 enhancer GRCh37_chr5:179461041-179462240 [Gene]
  • LOC129389422:MPRA-validated peak5609 silencer [Gene]
  • MRNIP:MRN complex interacting protein [Gene - OMIM - HGNC]
  • MRNIP-DT:MRNIP divergent transcript [Gene - HGNC]
  • LOC126807626:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:179245687-179246886 [Gene]
  • LOC126807629:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:179868388-179869587 [Gene]
  • RASGEF1C:RasGEF domain family member 1C [Gene - HGNC]
  • LOC123575638:Sharpr-MPRA regulatory region 14850 [Gene]
  • LOC112997583:Sharpr-MPRA regulatory region 15558 [Gene]
  • LOC112997584:Sharpr-MPRA regulatory region 4162 [Gene]
  • LOC123575637:Sharpr-MPRA regulatory region 4663 [Gene]
  • LOC123575636:Sharpr-MPRA regulatory region 5800 [Gene]
  • LOC121740635:Sharpr-MPRA regulatory region 8548 [Gene]
  • LOC123575639:Sharpr-MPRA regulatory region 9005 [Gene]
  • LOC123575635:Sharpr-MPRA regulatory region 9602 [Gene]
  • TBC1D9B:TBC1 domain family member 9B [Gene - OMIM - HGNC]
  • ZFP62:ZFP62 zinc finger protein [Gene - OMIM - HGNC]
  • MGAT1:alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase [Gene - OMIM - HGNC]
  • MGAT4B:alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B [Gene - OMIM - HGNC]
  • CANX:calnexin [Gene - OMIM - HGNC]
  • CBY3:chibby family member 3 [Gene - HGNC]
  • FLT4:fms related receptor tyrosine kinase 4 [Gene - OMIM - HGNC]
  • GFPT2:glutamine-fructose-6-phosphate transaminase 2 [Gene - OMIM - HGNC]
  • HEIH:hepatocellular carcinoma up-regulated EZH2-associated long non-coding RNA [Gene - OMIM - HGNC]
  • LTC4S:leukotriene C4 synthase [Gene - OMIM - HGNC]
  • LINC02222:long intergenic non-protein coding RNA 2222 [Gene - HGNC]
  • LINC00847:long intergenic non-protein coding RNA 847 [Gene - HGNC]
  • MAML1:mastermind like transcriptional coactivator 1 [Gene - OMIM - HGNC]
  • MIR1229:microRNA 1229 [Gene - HGNC]
  • MIR340:microRNA 340 [Gene - HGNC]
  • MAPK9:mitogen-activated protein kinase 9 [Gene - OMIM - HGNC]
  • OR2Y1:olfactory receptor family 2 subfamily Y member 1 [Gene - HGNC]
  • RNF130:ring finger protein 130 [Gene - OMIM - HGNC]
  • SCGB3A1:secretoglobin family 3A member 1 [Gene - OMIM - HGNC]
  • SQSTM1:sequestosome 1 [Gene - OMIM - HGNC]
  • LOC105377763:uncharacterized LOC105377763 [Gene]
Variant type:
copy number loss
Cytogenetic location:
5q35.3
Genomic location:
Preferred name:
GRCh38/hg38 5q35.3(chr5:179669736-180897169)x1
HGVS:
  • NC_000005.10:g.(?_179669736)_(180897169_?)del
  • NC_000005.8:g.(?_179029343)_(180256775_?)del
  • NC_000005.9:g.(?_179096737)_(180324169_?)del
Links:
dbVar: nssv585170; dbVar: nsv498459
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
SCV000174965GeneDx
no assertion criteria provided
Likely pathogenic
(Nov 30, 2010) 		not providedclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000174965.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providedyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Oct 14, 2023