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GRCh38/hg38 2p25.2-25.1(chr2:4416714-7632837)x1 AND See cases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 1, 2017
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:
RCV000133995.6

Allele description [Variation Report for GRCh38/hg38 2p25.2-25.1(chr2:4416714-7632837)x1]

GRCh38/hg38 2p25.2-25.1(chr2:4416714-7632837)x1

Genes:
  • LOC129933013:ATAC-STARR-seq lymphoblastoid active region 15240 [Gene]
  • LOC129933014:ATAC-STARR-seq lymphoblastoid active region 15241 [Gene]
  • LOC129933015:ATAC-STARR-seq lymphoblastoid active region 15242 [Gene]
  • LOC129933016:ATAC-STARR-seq lymphoblastoid active region 15243 [Gene]
  • LOC129933017:ATAC-STARR-seq lymphoblastoid active region 15244 [Gene]
  • LOC129933019:ATAC-STARR-seq lymphoblastoid active region 15245 [Gene]
  • LOC129933021:ATAC-STARR-seq lymphoblastoid active region 15246 [Gene]
  • LOC129933022:ATAC-STARR-seq lymphoblastoid active region 15247 [Gene]
  • LOC129933024:ATAC-STARR-seq lymphoblastoid active region 15248 [Gene]
  • LOC129933010:ATAC-STARR-seq lymphoblastoid silent region 11117 [Gene]
  • LOC129933011:ATAC-STARR-seq lymphoblastoid silent region 11118 [Gene]
  • LOC129933012:ATAC-STARR-seq lymphoblastoid silent region 11119 [Gene]
  • LOC129933018:ATAC-STARR-seq lymphoblastoid silent region 11120 [Gene]
  • LOC129933020:ATAC-STARR-seq lymphoblastoid silent region 11121 [Gene]
  • LOC129933023:ATAC-STARR-seq lymphoblastoid silent region 11122 [Gene]
  • LOC126806114:BRD4-independent group 4 enhancer GRCh37_chr2:5937560-5938759 [Gene]
  • LOC126806117:BRD4-independent group 4 enhancer GRCh37_chr2:6378134-6379333 [Gene]
  • LOC126806118:BRD4-independent group 4 enhancer GRCh37_chr2:6431337-6432536 [Gene]
  • LOC126806120:BRD4-independent group 4 enhancer GRCh37_chr2:6696453-6697652 [Gene]
  • LOC126806113:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:5390152-5391351 [Gene]
  • LOC126806115:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:6135557-6136756 [Gene]
  • LOC126806116:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:6232422-6233621 [Gene]
  • LOC126806121:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:6913298-6914497 [Gene]
  • LOC126806111:MED14-independent group 3 enhancer GRCh37_chr2:4635935-4637134 [Gene]
  • LOC126806112:MED14-independent group 3 enhancer GRCh37_chr2:4827862-4829061 [Gene]
  • LOC126806119:MED14-independent group 3 enhancer GRCh37_chr2:6677962-6679161 [Gene]
  • LOC126806122:MED14-independent group 3 enhancer GRCh37_chr2:7113462-7114661 [Gene]
  • MIR7515HG:MIR7515 host gene [Gene - HGNC]
  • LOC132088849:Neanderthal introgressed variant-containing enhancer experimental_58754 [Gene]
  • SOX11:SRY-box transcription factor 11 [Gene - OMIM - HGNC]
  • LOC120961741:Sharpr-MPRA regulatory region 11536 [Gene]
  • LOC122710288:Sharpr-MPRA regulatory region 3683 [Gene]
  • LOC122710287:Sharpr-MPRA regulatory region 7309 [Gene]
  • LOC111811968:Sharpr-MPRA regulatory region 7427/13434 [Gene]
  • LOC110121127:VISTA enhancer hs1496 [Gene]
  • CMPK2:cytidine/uridine monophosphate kinase 2 [Gene - OMIM - HGNC]
  • GRASLND:glycosaminoglycan regulatory associated long non-coding RNA [Gene - HGNC]
  • LINC01246:long intergenic non-protein coding RNA 1246 [Gene - HGNC]
  • LINC01247:long intergenic non-protein coding RNA 1247 [Gene - HGNC]
  • LINC01248:long intergenic non-protein coding RNA 1248 [Gene - HGNC]
  • LINC01249:long intergenic non-protein coding RNA 1249 [Gene - HGNC]
  • LINC01810:long intergenic non-protein coding RNA 1810 [Gene - HGNC]
  • LINC00487:long intergenic non-protein coding RNA 487 [Gene - HGNC]
  • MIR7158:microRNA 7158 [Gene - HGNC]
  • MIR7515:microRNA 7515 [Gene - HGNC]
  • NRIR:negative regulator of interferon response [Gene - OMIM - HGNC]
  • RSAD2:radical S-adenosyl methionine domain containing 2 [Gene - OMIM - HGNC]
  • RNF144A:ring finger protein 144A [Gene - OMIM - HGNC]
  • SILC1:sciatic injury induced lincRNA upregulator of SOX11 [Gene - HGNC]
  • LOC100506274:uncharacterized LOC100506274 [Gene]
  • LOC101929452:uncharacterized LOC101929452 [Gene]
  • LOC400940:uncharacterized LOC400940 [Gene]
Variant type:
copy number loss
Cytogenetic location:
2p25.2-25.1
Genomic location:
Preferred name:
GRCh38/hg38 2p25.2-25.1(chr2:4416714-7632837)x1
HGVS:
  • NC_000002.12:g.(?_4416714)_(7632837_?)del
  • NC_000002.10:g.(?_4442179)_(7690419_?)del
  • NC_000002.11:g.(?_4464304)_(7772968_?)del
Links:
dbVar: nssv575969; dbVar: nsv492060
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
SCV000173417ISCA site 4
no assertion criteria provided
Likely pathogenic
(Sep 1, 2017) 		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 4, SCV000173417.4

#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