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GRCh38/hg38 5p15.31-15.2(chr5:7670933-13623997)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 23, 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:
RCV000139904.6

Allele description [Variation Report for GRCh38/hg38 5p15.31-15.2(chr5:7670933-13623997)x1]

GRCh38/hg38 5p15.31-15.2(chr5:7670933-13623997)x1

Genes:
  • MTRR:5-methyltetrahydrofolate-homocysteine methyltransferase reductase [Gene - OMIM - HGNC]
  • LOC129993628:ATAC-STARR-seq lymphoblastoid active region 22344 [Gene]
  • LOC129993629:ATAC-STARR-seq lymphoblastoid active region 22345 [Gene]
  • LOC129993630:ATAC-STARR-seq lymphoblastoid active region 22346 [Gene]
  • LOC129993634:ATAC-STARR-seq lymphoblastoid active region 22347 [Gene]
  • LOC129993637:ATAC-STARR-seq lymphoblastoid active region 22348 [Gene]
  • LOC129993639:ATAC-STARR-seq lymphoblastoid active region 22349 [Gene]
  • LOC129993641:ATAC-STARR-seq lymphoblastoid active region 22350 [Gene]
  • LOC129993642:ATAC-STARR-seq lymphoblastoid active region 22351 [Gene]
  • LOC129993650:ATAC-STARR-seq lymphoblastoid active region 22352 [Gene]
  • LOC129993652:ATAC-STARR-seq lymphoblastoid active region 22353 [Gene]
  • LOC129993655:ATAC-STARR-seq lymphoblastoid active region 22354 [Gene]
  • LOC129993657:ATAC-STARR-seq lymphoblastoid active region 22355 [Gene]
  • LOC129993658:ATAC-STARR-seq lymphoblastoid active region 22356 [Gene]
  • LOC129993659:ATAC-STARR-seq lymphoblastoid active region 22360 [Gene]
  • LOC129993660:ATAC-STARR-seq lymphoblastoid active region 22361 [Gene]
  • LOC129993661:ATAC-STARR-seq lymphoblastoid active region 22362 [Gene]
  • LOC129993662:ATAC-STARR-seq lymphoblastoid active region 22363 [Gene]
  • LOC129993663:ATAC-STARR-seq lymphoblastoid active region 22364 [Gene]
  • LOC129993664:ATAC-STARR-seq lymphoblastoid active region 22366 [Gene]
  • LOC129993665:ATAC-STARR-seq lymphoblastoid active region 22367 [Gene]
  • LOC129993667:ATAC-STARR-seq lymphoblastoid active region 22368 [Gene]
  • LOC129993668:ATAC-STARR-seq lymphoblastoid active region 22369 [Gene]
  • LOC129993669:ATAC-STARR-seq lymphoblastoid active region 22370 [Gene]
  • LOC129993670:ATAC-STARR-seq lymphoblastoid active region 22371 [Gene]
  • LOC129993671:ATAC-STARR-seq lymphoblastoid active region 22375 [Gene]
  • LOC129993673:ATAC-STARR-seq lymphoblastoid active region 22376 [Gene]
  • LOC129993675:ATAC-STARR-seq lymphoblastoid active region 22377 [Gene]
  • LOC129993676:ATAC-STARR-seq lymphoblastoid active region 22378 [Gene]
  • LOC129993677:ATAC-STARR-seq lymphoblastoid active region 22379 [Gene]
  • LOC129993679:ATAC-STARR-seq lymphoblastoid active region 22381 [Gene]
  • LOC129993681:ATAC-STARR-seq lymphoblastoid active region 22382 [Gene]
  • LOC129993683:ATAC-STARR-seq lymphoblastoid active region 22383 [Gene]
  • LOC129993684:ATAC-STARR-seq lymphoblastoid active region 22384 [Gene]
  • LOC129993685:ATAC-STARR-seq lymphoblastoid active region 22385 [Gene]
  • LOC129993631:ATAC-STARR-seq lymphoblastoid silent region 15904 [Gene]
  • LOC129993632:ATAC-STARR-seq lymphoblastoid silent region 15905 [Gene]
  • LOC129993633:ATAC-STARR-seq lymphoblastoid silent region 15906 [Gene]
  • LOC129993635:ATAC-STARR-seq lymphoblastoid silent region 15907 [Gene]
  • LOC129993636:ATAC-STARR-seq lymphoblastoid silent region 15908 [Gene]
  • LOC129993638:ATAC-STARR-seq lymphoblastoid silent region 15909 [Gene]
  • LOC129993640:ATAC-STARR-seq lymphoblastoid silent region 15910 [Gene]
  • LOC129993643:ATAC-STARR-seq lymphoblastoid silent region 15911 [Gene]
  • LOC129993644:ATAC-STARR-seq lymphoblastoid silent region 15912 [Gene]
  • LOC129993645:ATAC-STARR-seq lymphoblastoid silent region 15913 [Gene]
  • LOC129993646:ATAC-STARR-seq lymphoblastoid silent region 15914 [Gene]
  • LOC129993647:ATAC-STARR-seq lymphoblastoid silent region 15915 [Gene]
  • LOC129993648:ATAC-STARR-seq lymphoblastoid silent region 15916 [Gene]
  • LOC129993649:ATAC-STARR-seq lymphoblastoid silent region 15917 [Gene]
  • LOC129993651:ATAC-STARR-seq lymphoblastoid silent region 15918 [Gene]
  • LOC129993653:ATAC-STARR-seq lymphoblastoid silent region 15919 [Gene]
  • LOC129993654:ATAC-STARR-seq lymphoblastoid silent region 15920 [Gene]
  • LOC129993656:ATAC-STARR-seq lymphoblastoid silent region 15921 [Gene]
  • LOC129993666:ATAC-STARR-seq lymphoblastoid silent region 15925 [Gene]
  • LOC129993672:ATAC-STARR-seq lymphoblastoid silent region 15926 [Gene]
  • LOC129993674:ATAC-STARR-seq lymphoblastoid silent region 15927 [Gene]
  • LOC129993678:ATAC-STARR-seq lymphoblastoid silent region 15928 [Gene]
  • LOC129993680:ATAC-STARR-seq lymphoblastoid silent region 15929 [Gene]
  • LOC129993682:ATAC-STARR-seq lymphoblastoid silent region 15930 [Gene]
  • ATPSCKMT:ATP synthase c subunit lysine N-methyltransferase [Gene - OMIM - HGNC]
  • LOC126807316:BRD4-independent group 4 enhancer GRCh37_chr5:11022334-11023533 [Gene]
  • LOC126807307:BRD4-independent group 4 enhancer GRCh37_chr5:7928453-7929652 [Gene]
  • LOC126807309:BRD4-independent group 4 enhancer GRCh37_chr5:8090277-8091476 [Gene]
  • LOC126807310:BRD4-independent group 4 enhancer GRCh37_chr5:8549695-8550894 [Gene]
  • LOC126807315:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:10595324-10596523 [Gene]
  • LOC126807308:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:7995658-7996857 [Gene]
  • LOC116158512:CRISPRi-validated cis-regulatory element chr5.702 [Gene]
  • DAP-DT:DAP divergent transcript [Gene - HGNC]
  • FASTKD3:FAST kinase domains 3 [Gene - OMIM - HGNC]
  • MARCHF6-DT:MARCHF6 divergent transcript [Gene - HGNC]
  • LOC126807314:MED14-independent group 3 enhancer GRCh37_chr5:10420944-10422143 [Gene]
  • LOC126807311:MED14-independent group 3 enhancer GRCh37_chr5:8828894-8830093 [Gene]
  • LOC126807312:MED14-independent group 3 enhancer GRCh37_chr5:9013731-9014930 [Gene]
  • LOC126807313:MED14-independent group 3 enhancer GRCh37_chr5:9775483-9776682 [Gene]
  • MIR4458HG:MIR4458 host gene [Gene - HGNC]
  • LOC132089161:Neanderthal introgressed variant-containing enhancer experimental_80752 [Gene]
  • LOC126807317:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:13567313-13568512 [Gene]
  • ROPN1L-AS1:ROPN1L antisense RNA 1 [Gene - HGNC]
  • SEMA5A-AS1:SEMA5A antisense RNA 1 [Gene - HGNC]
  • LOC123493268:Sharpr-MPRA regulatory region 11758 [Gene]
  • LOC123493266:Sharpr-MPRA regulatory region 1238 [Gene]
  • LOC112997551:Sharpr-MPRA regulatory region 12583 [Gene]
  • LOC112997550:Sharpr-MPRA regulatory region 12783 [Gene]
  • LOC123493265:Sharpr-MPRA regulatory region 1766 [Gene]
  • LOC123493267:Sharpr-MPRA regulatory region 1944 [Gene]
  • LOC111828522:Sharpr-MPRA regulatory regions 9329 and 12995 [Gene]
  • ADCY2:adenylate cyclase 2 [Gene - OMIM - HGNC]
  • ANKRD33B:ankyrin repeat domain 33B [Gene - HGNC]
  • CMBL:carboxymethylenebutenolidase homolog [Gene - OMIM - HGNC]
  • CTNND2:catenin delta 2 [Gene - OMIM - HGNC]
  • CCT5:chaperonin containing TCP1 subunit 5 [Gene - OMIM - HGNC]
  • CFAP90:cilia and flagella associated protein 90 [Gene - HGNC]
  • DAP:death associated protein [Gene - OMIM - HGNC]
  • LINC01194:long intergenic non-protein coding RNA 1194 [Gene - OMIM - HGNC]
  • LINC02112:long intergenic non-protein coding RNA 2112 [Gene - HGNC]
  • LINC02199:long intergenic non-protein coding RNA 2199 [Gene - HGNC]
  • LINC02212:long intergenic non-protein coding RNA 2212 [Gene - HGNC]
  • LINC02213:long intergenic non-protein coding RNA 2213 [Gene - HGNC]
  • LINC02220:long intergenic non-protein coding RNA 2220 [Gene - HGNC]
  • LINC02221:long intergenic non-protein coding RNA 2221 [Gene - HGNC]
  • LINC02226:long intergenic non-protein coding RNA 2226 [Gene - HGNC]
  • MARCHF6:membrane associated ring-CH-type finger 6 [Gene - OMIM - HGNC]
  • MIR10397:microRNA 10397 [Gene - HGNC]
  • MIR4458:microRNA 4458 [Gene - HGNC]
  • MIR4636:microRNA 4636 [Gene - HGNC]
  • MIR6131:microRNA 6131 [Gene - HGNC]
  • ROPN1L:rhophilin associated tail protein 1 like [Gene - OMIM - HGNC]
  • SEMA5A:semaphorin 5A [Gene - OMIM - HGNC]
  • SNHG18:small nucleolar RNA host gene 18 [Gene - HGNC]
  • SNORD123:small nucleolar RNA, C/D box 123 [Gene - HGNC]
  • TAS2R1:taste 2 receptor member 1 [Gene - OMIM - HGNC]
  • CTD-2154B17.1:uncharacterized CTD-2154B17.1 [Gene]
  • LOC105374647:uncharacterized LOC105374647 [Gene]
  • LOC105374655:uncharacterized LOC105374655 [Gene]
Variant type:
copy number loss
Cytogenetic location:
5p15.31-15.2
Genomic location:
Preferred name:
GRCh38/hg38 5p15.31-15.2(chr5:7670933-13623997)x1
HGVS:
  • NC_000005.10:g.(?_7670933)_(13623997_?)del
  • NC_000005.8:g.(?_7724046)_(13677106_?)del
  • NC_000005.9:g.(?_7671046)_(13624106_?)del
Links:
dbVar: nssv1608889; dbVar: nsv931046
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
SCV000180545ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Oct 23, 2012) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot 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, SCV000180545.4

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

Last Updated: May 7, 2024