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GRCh38/hg38 3q29(chr3:196013531-197590232)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 21, 2012
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:
RCV000138573.5

Allele description [Variation Report for GRCh38/hg38 3q29(chr3:196013531-197590232)x1]

GRCh38/hg38 3q29(chr3:196013531-197590232)x1

Genes:
  • BDH1:3-hydroxybutyrate dehydrogenase 1 [Gene - OMIM - HGNC]
  • LOC129938264:ATAC-STARR-seq lymphoblastoid active region 21065 [Gene]
  • LOC129938267:ATAC-STARR-seq lymphoblastoid active region 21066 [Gene]
  • LOC129938268:ATAC-STARR-seq lymphoblastoid active region 21067 [Gene]
  • LOC129938269:ATAC-STARR-seq lymphoblastoid active region 21068 [Gene]
  • LOC129938270:ATAC-STARR-seq lymphoblastoid active region 21069 [Gene]
  • LOC129938272:ATAC-STARR-seq lymphoblastoid active region 21070 [Gene]
  • LOC129938273:ATAC-STARR-seq lymphoblastoid active region 21071 [Gene]
  • LOC129938274:ATAC-STARR-seq lymphoblastoid active region 21072 [Gene]
  • LOC129938275:ATAC-STARR-seq lymphoblastoid active region 21076 [Gene]
  • LOC129938276:ATAC-STARR-seq lymphoblastoid active region 21077 [Gene]
  • LOC129938279:ATAC-STARR-seq lymphoblastoid active region 21081 [Gene]
  • LOC129938280:ATAC-STARR-seq lymphoblastoid active region 21082 [Gene]
  • LOC129938281:ATAC-STARR-seq lymphoblastoid active region 21083 [Gene]
  • LOC129938283:ATAC-STARR-seq lymphoblastoid active region 21086 [Gene]
  • LOC129938285:ATAC-STARR-seq lymphoblastoid active region 21087 [Gene]
  • LOC129938288:ATAC-STARR-seq lymphoblastoid active region 21090 [Gene]
  • LOC129938289:ATAC-STARR-seq lymphoblastoid active region 21091 [Gene]
  • LOC129938290:ATAC-STARR-seq lymphoblastoid active region 21092 [Gene]
  • LOC129938292:ATAC-STARR-seq lymphoblastoid active region 21095 [Gene]
  • LOC129938295:ATAC-STARR-seq lymphoblastoid active region 21096 [Gene]
  • LOC129938298:ATAC-STARR-seq lymphoblastoid active region 21097 [Gene]
  • LOC129938299:ATAC-STARR-seq lymphoblastoid active region 21098 [Gene]
  • LOC129938300:ATAC-STARR-seq lymphoblastoid active region 21099 [Gene]
  • LOC129938301:ATAC-STARR-seq lymphoblastoid active region 21100 [Gene]
  • LOC129938302:ATAC-STARR-seq lymphoblastoid active region 21101 [Gene]
  • LOC129938305:ATAC-STARR-seq lymphoblastoid active region 21106 [Gene]
  • LOC129938309:ATAC-STARR-seq lymphoblastoid active region 21107 [Gene]
  • LOC129938314:ATAC-STARR-seq lymphoblastoid active region 21108 [Gene]
  • LOC129938315:ATAC-STARR-seq lymphoblastoid active region 21111 [Gene]
  • LOC129938261:ATAC-STARR-seq lymphoblastoid silent region 15051 [Gene]
  • LOC129938262:ATAC-STARR-seq lymphoblastoid silent region 15052 [Gene]
  • LOC129938263:ATAC-STARR-seq lymphoblastoid silent region 15053 [Gene]
  • LOC129938265:ATAC-STARR-seq lymphoblastoid silent region 15054 [Gene]
  • LOC129938266:ATAC-STARR-seq lymphoblastoid silent region 15055 [Gene]
  • LOC129938271:ATAC-STARR-seq lymphoblastoid silent region 15056 [Gene]
  • LOC129938277:ATAC-STARR-seq lymphoblastoid silent region 15057 [Gene]
  • LOC129938278:ATAC-STARR-seq lymphoblastoid silent region 15058 [Gene]
  • LOC129938282:ATAC-STARR-seq lymphoblastoid silent region 15059 [Gene]
  • LOC129938284:ATAC-STARR-seq lymphoblastoid silent region 15060 [Gene]
  • LOC129938286:ATAC-STARR-seq lymphoblastoid silent region 15063 [Gene]
  • LOC129938287:ATAC-STARR-seq lymphoblastoid silent region 15064 [Gene]
  • LOC129938291:ATAC-STARR-seq lymphoblastoid silent region 15065 [Gene]
  • LOC129938293:ATAC-STARR-seq lymphoblastoid silent region 15066 [Gene]
  • LOC129938294:ATAC-STARR-seq lymphoblastoid silent region 15067 [Gene]
  • LOC129938296:ATAC-STARR-seq lymphoblastoid silent region 15069 [Gene]
  • LOC129938297:ATAC-STARR-seq lymphoblastoid silent region 15070 [Gene]
  • LOC129938303:ATAC-STARR-seq lymphoblastoid silent region 15072 [Gene]
  • LOC129938304:ATAC-STARR-seq lymphoblastoid silent region 15073 [Gene]
  • LOC129938306:ATAC-STARR-seq lymphoblastoid silent region 15080 [Gene]
  • LOC129938307:ATAC-STARR-seq lymphoblastoid silent region 15081 [Gene]
  • LOC129938308:ATAC-STARR-seq lymphoblastoid silent region 15082 [Gene]
  • LOC129938310:ATAC-STARR-seq lymphoblastoid silent region 15083 [Gene]
  • LOC129938311:ATAC-STARR-seq lymphoblastoid silent region 15084 [Gene]
  • LOC129938312:ATAC-STARR-seq lymphoblastoid silent region 15086 [Gene]
  • LOC129938313:ATAC-STARR-seq lymphoblastoid silent region 15087 [Gene]
  • LOC126806932:BRD4-independent group 4 enhancer GRCh37_chr3:195973646-195974845 [Gene]
  • LOC112935924:BRD4-independent group 4 enhancer GRCh37_chr3:196064783-196065982 [Gene]
  • LOC126806934:BRD4-independent group 4 enhancer GRCh37_chr3:196293567-196294766 [Gene]
  • LOC121048736:BRD4-independent group 4 enhancer GRCh37_chr3:196758105-196759304 [Gene]
  • LOC126806935:BRD4-independent group 4 enhancer GRCh37_chr3:197136564-197137763 [Gene]
  • LOC126806936:BRD4-independent group 4 enhancer GRCh37_chr3:197205169-197206368 [Gene]
  • LOC115995537:CRISPRi-validated cis-regulatory element chr3.5812 [Gene]
  • LOC115995538:CRISPRi-validated cis-regulatory element chr3.5817 [Gene]
  • DLG1-AS1:DLG1 antisense RNA 1 [Gene - HGNC]
  • FBXO45:F-box protein 45 [Gene - OMIM - HGNC]
  • LOC123464504:H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:197216831-197217376 and GRCh37_chr3:197217377-197217922 [Gene]
  • LOC126806933:MED14-independent group 3 enhancer GRCh37_chr3:196289997-196291196 [Gene]
  • MELTF-AS1:MELTF antisense RNA 1 [Gene - HGNC]
  • LOC129389196:MPRA-validated peak4992 silencer [Gene]
  • LOC129389197:MPRA-validated peak4993 silencer [Gene]
  • NCBP2AS2:NCBP2 antisense 2 (head to head) [Gene - HGNC]
  • NCBP2-AS1:NCBP2 antisense RNA 1 [Gene - HGNC]
  • LOC111828515:OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:197268447-197269042 [Gene]
  • LOC121725167:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:197121050-197122249 [Gene]
  • SENP5:SUMO specific peptidase 5 [Gene - OMIM - HGNC]
  • LOC123464501:Sharpr-MPRA regulatory region 11589 [Gene]
  • LOC123464503:Sharpr-MPRA regulatory region 1192 [Gene]
  • LOC123464502:Sharpr-MPRA regulatory region 2091 [Gene]
  • LOC123464500:Sharpr-MPRA regulatory region 363 [Gene]
  • LOC123464499:Sharpr-MPRA regulatory region 4041 [Gene]
  • LOC123464505:Sharpr-MPRA regulatory region 5776 [Gene]
  • LOC123464498:Sharpr-MPRA regulatory region 7098 [Gene]
  • TM4SF19-AS1:TM4SF19 antisense RNA 1 [Gene - HGNC]
  • TM4SF19-DYNLT2B:TM4SF19-DYNLT2B readthrough (NMD candidate) [Gene - HGNC]
  • UBXN7:UBX domain protein 7 [Gene - OMIM - HGNC]
  • UBXN7-AS1:UBXN7 antisense RNA 1 [Gene - HGNC]
  • WDR53:WD repeat domain 53 [Gene - OMIM - HGNC]
  • CEP19:centrosomal protein 19 [Gene - OMIM - HGNC]
  • DLG1:discs large MAGUK scaffold protein 1 [Gene - OMIM - HGNC]
  • DYNLT2B:dynein light chain Tctex-type 2B [Gene - OMIM - HGNC]
  • LINC01063:long intergenic non-protein coding RNA 1063 [Gene - HGNC]
  • LINC02012:long intergenic non-protein coding RNA 2012 [Gene - HGNC]
  • LINC00885:long intergenic non-protein coding RNA 885 [Gene - HGNC]
  • MELTF:melanotransferrin [Gene - OMIM - HGNC]
  • MIR4797:microRNA 4797 [Gene - HGNC]
  • NRROS:negative regulator of reactive oxygen species [Gene - OMIM - HGNC]
  • NCBP2:nuclear cap binding protein subunit 2 [Gene - OMIM - HGNC]
  • PAK2:p21 (RAC1) activated kinase 2 [Gene - OMIM - HGNC]
  • PCYT1A:phosphate cytidylyltransferase 1A, choline [Gene - OMIM - HGNC]
  • PIGX:phosphatidylinositol glycan anchor biosynthesis class X [Gene - OMIM - HGNC]
  • PIGZ:phosphatidylinositol glycan anchor biosynthesis class Z [Gene - OMIM - HGNC]
  • RNF168:ring finger protein 168 [Gene - OMIM - HGNC]
  • SMCO1:single-pass membrane protein with coiled-coil domains 1 [Gene - HGNC]
  • SLC51A:solute carrier family 51 member A [Gene - OMIM - HGNC]
  • TFRC:transferrin receptor [Gene - OMIM - HGNC]
  • TM4SF19:transmembrane 4 L six family member 19 [Gene - OMIM - HGNC]
  • LOC105374308:uncharacterized LOC105374308 [Gene]
  • ZDHHC19:zinc finger DHHC-type palmitoyltransferase 19 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
3q29
Genomic location:
Preferred name:
GRCh38/hg38 3q29(chr3:196013531-197590232)x1
HGVS:
  • NC_000003.12:g.(?_196013531)_(197590232_?)del
  • NC_000003.10:g.(?_197224799)_(198801500_?)del
  • NC_000003.11:g.(?_195740402)_(197317103_?)del
Links:
dbVar: nssv1601953; dbVar: nssv1604878; dbVar: nsv915835
Observations:
2

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
SCV000178932ISCA site 4

See additional submitters

no assertion criteria provided
Pathogenic
(Sep 21, 2012) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes2not providednot providednot providednot providedclinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]
PMID:
20466091
PMCID:
PMC2869000

Details of each submission

From ISCA site 4, SCV000178932.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
2not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided
2unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Sep 1, 2024