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GRCh38/hg38 5p13.3-13.2(chr5:30961310-36143306)x1 AND See cases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 5, 2011
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:
RCV000135667.7

Allele description [Variation Report for GRCh38/hg38 5p13.3-13.2(chr5:30961310-36143306)x1]

GRCh38/hg38 5p13.3-13.2(chr5:30961310-36143306)x1

Genes:
  • ADAMTS12:ADAM metallopeptidase with thrombospondin type 1 motif 12 [Gene - OMIM - HGNC]
  • LOC129993745:ATAC-STARR-seq lymphoblastoid active region 22431 [Gene]
  • LOC129993746:ATAC-STARR-seq lymphoblastoid active region 22432 [Gene]
  • LOC129993747:ATAC-STARR-seq lymphoblastoid active region 22433 [Gene]
  • LOC129993749:ATAC-STARR-seq lymphoblastoid active region 22434 [Gene]
  • LOC129993750:ATAC-STARR-seq lymphoblastoid active region 22435 [Gene]
  • LOC129993751:ATAC-STARR-seq lymphoblastoid active region 22436 [Gene]
  • LOC129993754:ATAC-STARR-seq lymphoblastoid active region 22438 [Gene]
  • LOC129993755:ATAC-STARR-seq lymphoblastoid active region 22439 [Gene]
  • LOC129993756:ATAC-STARR-seq lymphoblastoid active region 22440 [Gene]
  • LOC129993757:ATAC-STARR-seq lymphoblastoid active region 22441 [Gene]
  • LOC129993758:ATAC-STARR-seq lymphoblastoid active region 22442 [Gene]
  • LOC129993759:ATAC-STARR-seq lymphoblastoid active region 22443 [Gene]
  • LOC129993762:ATAC-STARR-seq lymphoblastoid active region 22444 [Gene]
  • LOC129993764:ATAC-STARR-seq lymphoblastoid active region 22445 [Gene]
  • LOC129993765:ATAC-STARR-seq lymphoblastoid active region 22446 [Gene]
  • LOC129993766:ATAC-STARR-seq lymphoblastoid active region 22447 [Gene]
  • LOC129993767:ATAC-STARR-seq lymphoblastoid active region 22448 [Gene]
  • LOC129993768:ATAC-STARR-seq lymphoblastoid active region 22449 [Gene]
  • LOC129993769:ATAC-STARR-seq lymphoblastoid active region 22450 [Gene]
  • LOC129993770:ATAC-STARR-seq lymphoblastoid active region 22451 [Gene]
  • LOC129993771:ATAC-STARR-seq lymphoblastoid active region 22452 [Gene]
  • LOC129993776:ATAC-STARR-seq lymphoblastoid active region 22454 [Gene]
  • LOC129993777:ATAC-STARR-seq lymphoblastoid active region 22455 [Gene]
  • LOC129993779:ATAC-STARR-seq lymphoblastoid active region 22456 [Gene]
  • LOC129993781:ATAC-STARR-seq lymphoblastoid active region 22457 [Gene]
  • LOC129993782:ATAC-STARR-seq lymphoblastoid active region 22460 [Gene]
  • LOC129993783:ATAC-STARR-seq lymphoblastoid active region 22461 [Gene]
  • LOC129993784:ATAC-STARR-seq lymphoblastoid active region 22462 [Gene]
  • LOC129993785:ATAC-STARR-seq lymphoblastoid active region 22463 [Gene]
  • LOC129993786:ATAC-STARR-seq lymphoblastoid active region 22464 [Gene]
  • LOC129993788:ATAC-STARR-seq lymphoblastoid active region 22465 [Gene]
  • LOC129993789:ATAC-STARR-seq lymphoblastoid active region 22466 [Gene]
  • LOC129993793:ATAC-STARR-seq lymphoblastoid active region 22470 [Gene]
  • LOC129993794:ATAC-STARR-seq lymphoblastoid active region 22471 [Gene]
  • LOC129993795:ATAC-STARR-seq lymphoblastoid active region 22472 [Gene]
  • LOC129993796:ATAC-STARR-seq lymphoblastoid active region 22473 [Gene]
  • LOC129993797:ATAC-STARR-seq lymphoblastoid active region 22474 [Gene]
  • LOC129993798:ATAC-STARR-seq lymphoblastoid active region 22475 [Gene]
  • LOC129993748:ATAC-STARR-seq lymphoblastoid silent region 15952 [Gene]
  • LOC129993752:ATAC-STARR-seq lymphoblastoid silent region 15953 [Gene]
  • LOC129993753:ATAC-STARR-seq lymphoblastoid silent region 15954 [Gene]
  • LOC129993760:ATAC-STARR-seq lymphoblastoid silent region 15955 [Gene]
  • LOC129993761:ATAC-STARR-seq lymphoblastoid silent region 15956 [Gene]
  • LOC129993763:ATAC-STARR-seq lymphoblastoid silent region 15958 [Gene]
  • LOC129993772:ATAC-STARR-seq lymphoblastoid silent region 15959 [Gene]
  • LOC129993773:ATAC-STARR-seq lymphoblastoid silent region 15960 [Gene]
  • LOC129993774:ATAC-STARR-seq lymphoblastoid silent region 15961 [Gene]
  • LOC129993775:ATAC-STARR-seq lymphoblastoid silent region 15962 [Gene]
  • LOC129993778:ATAC-STARR-seq lymphoblastoid silent region 15963 [Gene]
  • LOC129993780:ATAC-STARR-seq lymphoblastoid silent region 15964 [Gene]
  • LOC129993787:ATAC-STARR-seq lymphoblastoid silent region 15966 [Gene]
  • LOC129993790:ATAC-STARR-seq lymphoblastoid silent region 15967 [Gene]
  • LOC129993791:ATAC-STARR-seq lymphoblastoid silent region 15968 [Gene]
  • LOC129993792:ATAC-STARR-seq lymphoblastoid silent region 15969 [Gene]
  • LOC126807342:BRD4-independent group 4 enhancer GRCh37_chr5:31342590-31343789 [Gene]
  • LOC126807348:BRD4-independent group 4 enhancer GRCh37_chr5:33460526-33461725 [Gene]
  • LOC126807351:BRD4-independent group 4 enhancer GRCh37_chr5:33612245-33613444 [Gene]
  • LOC126807352:BRD4-independent group 4 enhancer GRCh37_chr5:33788320-33789519 [Gene]
  • LOC126807357:BRD4-independent group 4 enhancer GRCh37_chr5:35788726-35789925 [Gene]
  • C1QTNF3-AMACR:C1QTNF3-AMACR readthrough (NMD candidate) [Gene - HGNC]
  • C1QTNF3:C1q and TNF related 3 [Gene - OMIM - HGNC]
  • CAPSL-DT:CAPSL divergent transcript [Gene - HGNC]
  • LOC126807340:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:31053108-31054307 [Gene]
  • LOC126807341:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:31119151-31120350 [Gene]
  • LOC126807343:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:32097810-32099009 [Gene]
  • LOC126807344:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:32125750-32126949 [Gene]
  • LOC126807345:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:32653566-32654765 [Gene]
  • LOC126807349:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:33576148-33577347 [Gene]
  • LOC126807353:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:34502110-34503309 [Gene]
  • LOC126807354:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:34866693-34867892 [Gene]
  • DNAJC21:DnaJ heat shock protein family (Hsp40) member C21 [Gene - OMIM - HGNC]
  • LMBRD2:LMBR1 domain containing 2 [Gene - OMIM - HGNC]
  • LOC126807347:MED14-independent group 3 enhancer GRCh37_chr5:33311980-33313179 [Gene]
  • LOC126807350:MED14-independent group 3 enhancer GRCh37_chr5:33604013-33605212 [Gene]
  • LOC126807355:MED14-independent group 3 enhancer GRCh37_chr5:34922818-34924017 [Gene]
  • LOC126807356:MED14-independent group 3 enhancer GRCh37_chr5:35117544-35118743 [Gene]
  • LOC129389269:MPRA-validated peak5220 silencer [Gene]
  • LOC129389270:MPRA-validated peak5221 silencer [Gene]
  • LOC129389271:MPRA-validated peak5222 silencer [Gene]
  • LOC129389272:MPRA-validated peak5224 silencer [Gene]
  • LOC114803477:MTMR12 eExon liver enhancer [Gene]
  • LOC108281130:NPR3 intron CAGE-defined low expression enhancer [Gene]
  • LOC132089242:Neanderthal introgressed variant-containing enhancer experimental_84469 [Gene]
  • LOC132089243:Neanderthal introgressed variant-containing enhancer experimental_84483 [Gene]
  • LOC123493286:OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:34412131-34412953 [Gene]
  • LOC126807346:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:32767828-32769027 [Gene]
  • PDZD2:PDZ domain containing 2 [Gene - OMIM - HGNC]
  • RAD1:RAD1 checkpoint DNA exonuclease [Gene - OMIM - HGNC]
  • RAI14-DT:RAI14 divergent transcript [Gene - HGNC]
  • SUB1:SUB1 regulator of transcription [Gene - OMIM - HGNC]
  • LOC123493288:Sharpr-MPRA regulatory region 11164 [Gene]
  • LOC121725199:Sharpr-MPRA regulatory region 11513 [Gene]
  • LOC123493285:Sharpr-MPRA regulatory region 14601 [Gene]
  • LOC123493284:Sharpr-MPRA regulatory region 158 [Gene]
  • LOC123493283:Sharpr-MPRA regulatory region 2864 [Gene]
  • LOC123493287:Sharpr-MPRA regulatory region 5567 [Gene]
  • LOC123493282:Sharpr-MPRA regulatory region 6191 [Gene]
  • LOC121725200:Sharpr-MPRA regulatory region 6534 [Gene]
  • LOC123493289:Sharpr-MPRA regulatory region 7256 [Gene]
  • LOC114004392:Sharpr-MPRA regulatory region 7574 [Gene]
  • TTC23L-AS1:TTC23L antisense RNA 1 [Gene - HGNC]
  • UGT3A1:UDP glycosyltransferase family 3 member A1 [Gene - OMIM - HGNC]
  • UGT3A2:UDP glycosyltransferase family 3 member A2 [Gene - OMIM - HGNC]
  • LOC114827820:VISTA enhancer hs1312 [Gene]
  • AGXT2:alanine--glyoxylate aminotransferase 2 [Gene - OMIM - HGNC]
  • AMACR:alpha-methylacyl-CoA racemase [Gene - OMIM - HGNC]
  • BRIX1:biogenesis of ribosomes BRX1 [Gene - OMIM - HGNC]
  • CDH6:cadherin 6 [Gene - OMIM - HGNC]
  • CAPSL:calcyphosine like [Gene - OMIM - HGNC]
  • C5orf22:chromosome 5 open reading frame 22 [Gene - HGNC]
  • DROSHA:drosha ribonuclease III [Gene - OMIM - HGNC]
  • GOLPH3:golgi phosphoprotein 3 [Gene - OMIM - HGNC]
  • IL7R:interleukin 7 receptor [Gene - OMIM - HGNC]
  • LINC02061:long intergenic non-protein coding RNA 2061 [Gene - HGNC]
  • LINC02120:long intergenic non-protein coding RNA 2120 [Gene - HGNC]
  • LINC02160:long intergenic non-protein coding RNA 2160 [Gene - HGNC]
  • MIR4279:microRNA 4279 [Gene - HGNC]
  • MIR579:microRNA 579 [Gene - HGNC]
  • MTMR12:myotubularin related protein 12 [Gene - OMIM - HGNC]
  • NPR3:natriuretic peptide receptor 3 [Gene - OMIM - HGNC]
  • PRLR:prolactin receptor [Gene - OMIM - HGNC]
  • RXFP3:relaxin family peptide receptor 3 [Gene - OMIM - HGNC]
  • RAI14:retinoic acid induced 14 [Gene - OMIM - HGNC]
  • SLC45A2:solute carrier family 45 member 2 [Gene - OMIM - HGNC]
  • SPEF2:sperm flagellar 2 [Gene - OMIM - HGNC]
  • TTC23L:tetratricopeptide repeat domain 23 like [Gene - OMIM - HGNC]
  • TARS1:threonyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
  • LOC105374715:uncharacterized LOC105374715 [Gene]
  • ZFR:zinc finger RNA binding protein [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
5p13.3-13.2
Genomic location:
Preferred name:
GRCh38/hg38 5p13.3-13.2(chr5:30961310-36143306)x1
HGVS:
  • NC_000005.10:g.(?_30961310)_(36143306_?)del
  • NC_000005.8:g.(?_30997174)_(36179165_?)del
  • NC_000005.9:g.(?_30961417)_(36143408_?)del
Links:
dbVar: nssv706419; dbVar: nsv530508
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
SCV000175549ISCA site 1

See additional submitters

no assertion criteria provided
Likely pathogenic
(Aug 5, 2011) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
humannot providedyes1not 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 1, SCV000175549.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1human1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024