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GRCh38/hg38 2p25.3(chr2:39193-1542734)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 1, 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:
RCV000136750.5

Allele description [Variation Report for GRCh38/hg38 2p25.3(chr2:39193-1542734)x1]

GRCh38/hg38 2p25.3(chr2:39193-1542734)x1

Genes:
  • ALKAL2:ALK and LTK ligand 2 [Gene - OMIM - HGNC]
  • LOC129932975:ATAC-STARR-seq lymphoblastoid active region 15215 [Gene]
  • LOC129932977:ATAC-STARR-seq lymphoblastoid active region 15217 [Gene]
  • LOC129932978:ATAC-STARR-seq lymphoblastoid active region 15218 [Gene]
  • LOC129932979:ATAC-STARR-seq lymphoblastoid active region 15219 [Gene]
  • LOC129932973:ATAC-STARR-seq lymphoblastoid silent region 11098 [Gene]
  • LOC129932974:ATAC-STARR-seq lymphoblastoid silent region 11099 [Gene]
  • LOC129932976:ATAC-STARR-seq lymphoblastoid silent region 11100 [Gene]
  • LOC129932980:ATAC-STARR-seq lymphoblastoid silent region 11102 [Gene]
  • LOC126806102:BRD4-independent group 4 enhancer GRCh37_chr2:1265169-1266368 [Gene]
  • LOC126806099:BRD4-independent group 4 enhancer GRCh37_chr2:850078-851277 [Gene]
  • LOC126806101:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:1104105-1105304 [Gene]
  • LOC126806104:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:1544276-1545475 [Gene]
  • LOC126806091:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:162049-163248 [Gene]
  • LOC126806093:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:284666-285865 [Gene]
  • LOC126806098:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:608557-609756 [Gene]
  • LOC126806100:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:863929-865128 [Gene]
  • LOC126806092:MED14-independent group 3 enhancer GRCh37_chr2:197602-198801 [Gene]
  • LOC126806094:MED14-independent group 3 enhancer GRCh37_chr2:373572-374771 [Gene]
  • LOC126806095:MED14-independent group 3 enhancer GRCh37_chr2:495062-496261 [Gene]
  • LOC126806096:MED14-independent group 3 enhancer GRCh37_chr2:582585-583784 [Gene]
  • LOC129388814:MPRA-validated peak3578 silencer [Gene]
  • LOC129388815:MPRA-validated peak3579 silencer [Gene]
  • LOC132088846:Neanderthal introgressed variant-containing enhancer experimental_58516 [Gene]
  • LOC126806103:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:1421072-1422271 [Gene]
  • LOC126806097:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:602328-603527 [Gene]
  • SH3YL1:SH3 and SYLF domain containing 1 [Gene - OMIM - HGNC]
  • SNTG2-AS1:SNTG2 antisense RNA 1 [Gene - HGNC]
  • LOC122710286:Sharpr-MPRA regulatory region 1386 [Gene]
  • TMEM18-DT:TMEM18 divergent transcript [Gene - HGNC]
  • ACP1:acid phosphatase 1 [Gene - OMIM - HGNC]
  • FAM110C:family with sequence similarity 110 member C [Gene - OMIM - HGNC]
  • LINC01115:long intergenic non-protein coding RNA 1115 [Gene - HGNC]
  • LINC01865:long intergenic non-protein coding RNA 1865 [Gene - HGNC]
  • LINC01874:long intergenic non-protein coding RNA 1874 [Gene - HGNC]
  • LINC01875:long intergenic non-protein coding RNA 1875 [Gene - HGNC]
  • LINC01939:long intergenic non-protein coding RNA 1939 [Gene - HGNC]
  • SNTG2:syntrophin gamma 2 [Gene - OMIM - HGNC]
  • TPO:thyroid peroxidase [Gene - OMIM - HGNC]
  • TMEM18:transmembrane protein 18 [Gene - OMIM - HGNC]
  • LOC100996637:uncharacterized LOC100996637 [Gene]
  • LOC105373346:uncharacterized LOC105373346 [Gene]
  • LOC105373352:uncharacterized LOC105373352 [Gene]
Variant type:
copy number loss
Cytogenetic location:
2p25.3
Genomic location:
Preferred name:
GRCh38/hg38 2p25.3(chr2:39193-1542734)x1
HGVS:
  • NC_000002.12:g.(?_39193)_(1542734_?)del
  • NC_000002.10:g.(?_29193)_(1525513_?)del
  • NC_000002.11:g.(?_39193)_(1546506_?)del
Links:
dbVar: nssv582137; dbVar: nsv534093
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
SCV000176870ISCA site 8

See additional submitters

no assertion criteria provided
Pathogenic
(Oct 1, 2010) 		maternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyes1not 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 8, SCV000176870.3

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

Last Updated: Sep 1, 2024