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GRCh38/hg38 2p25.3-25.2(chr2:30341-4642399)x3 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 16, 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:
RCV000142735.6

Allele description [Variation Report for GRCh38/hg38 2p25.3-25.2(chr2:30341-4642399)x3]

GRCh38/hg38 2p25.3-25.2(chr2:30341-4642399)x3

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]
  • LOC129932984:ATAC-STARR-seq lymphoblastoid active region 15220 [Gene]
  • LOC129932987:ATAC-STARR-seq lymphoblastoid active region 15221 [Gene]
  • LOC129932988:ATAC-STARR-seq lymphoblastoid active region 15222 [Gene]
  • LOC129932989:ATAC-STARR-seq lymphoblastoid active region 15223 [Gene]
  • LOC129932990:ATAC-STARR-seq lymphoblastoid active region 15224 [Gene]
  • LOC129932991:ATAC-STARR-seq lymphoblastoid active region 15225 [Gene]
  • LOC129932992:ATAC-STARR-seq lymphoblastoid active region 15226 [Gene]
  • LOC129932993:ATAC-STARR-seq lymphoblastoid active region 15227 [Gene]
  • LOC129932994:ATAC-STARR-seq lymphoblastoid active region 15228 [Gene]
  • LOC129932995:ATAC-STARR-seq lymphoblastoid active region 15229 [Gene]
  • LOC129933000:ATAC-STARR-seq lymphoblastoid active region 15230 [Gene]
  • LOC129933002:ATAC-STARR-seq lymphoblastoid active region 15231 [Gene]
  • LOC129933004:ATAC-STARR-seq lymphoblastoid active region 15232 [Gene]
  • LOC129933005:ATAC-STARR-seq lymphoblastoid active region 15233 [Gene]
  • LOC129933006:ATAC-STARR-seq lymphoblastoid active region 15234 [Gene]
  • LOC129933007:ATAC-STARR-seq lymphoblastoid active region 15235 [Gene]
  • LOC129933008:ATAC-STARR-seq lymphoblastoid active region 15236 [Gene]
  • LOC129933009:ATAC-STARR-seq lymphoblastoid active region 15238 [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]
  • LOC129932981:ATAC-STARR-seq lymphoblastoid silent region 11103 [Gene]
  • LOC129932982:ATAC-STARR-seq lymphoblastoid silent region 11104 [Gene]
  • LOC129932983:ATAC-STARR-seq lymphoblastoid silent region 11105 [Gene]
  • LOC129932985:ATAC-STARR-seq lymphoblastoid silent region 11106 [Gene]
  • LOC129932986:ATAC-STARR-seq lymphoblastoid silent region 11107 [Gene]
  • LOC129932996:ATAC-STARR-seq lymphoblastoid silent region 11108 [Gene]
  • LOC129932997:ATAC-STARR-seq lymphoblastoid silent region 11109 [Gene]
  • LOC129932998:ATAC-STARR-seq lymphoblastoid silent region 11110 [Gene]
  • LOC129932999:ATAC-STARR-seq lymphoblastoid silent region 11111 [Gene]
  • LOC129933001:ATAC-STARR-seq lymphoblastoid silent region 11114 [Gene]
  • LOC129933003:ATAC-STARR-seq lymphoblastoid silent region 11115 [Gene]
  • LOC129933010:ATAC-STARR-seq lymphoblastoid silent region 11117 [Gene]
  • LOC126806102:BRD4-independent group 4 enhancer GRCh37_chr2:1265169-1266368 [Gene]
  • LOC126806107:BRD4-independent group 4 enhancer GRCh37_chr2:3034172-3035371 [Gene]
  • LOC126806108:BRD4-independent group 4 enhancer GRCh37_chr2:3237853-3239052 [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]
  • LOC126806106:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:2952587-2953786 [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]
  • EIPR1:EARP complex and GARP complex interacting protein 1 [Gene - OMIM - HGNC]
  • LOC126806092:MED14-independent group 3 enhancer GRCh37_chr2:197602-198801 [Gene]
  • LOC121725078:MED14-independent group 3 enhancer GRCh37_chr2:3583482-3584681 [Gene]
  • LOC126806094:MED14-independent group 3 enhancer GRCh37_chr2:373572-374771 [Gene]
  • LOC126806109:MED14-independent group 3 enhancer GRCh37_chr2:4033381-4034580 [Gene]
  • LOC126806110:MED14-independent group 3 enhancer GRCh37_chr2:4268419-4269618 [Gene]
  • LOC126806111:MED14-independent group 3 enhancer GRCh37_chr2:4635935-4637134 [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]
  • LOC129388816:MPRA-validated peak3584 silencer [Gene]
  • MYT1L-AS1:MYT1L antisense RNA 1 [Gene - HGNC]
  • LOC132088839:Neanderthal introgressed variant-containing enhancer experimental_58239 [Gene]
  • LOC132088841:Neanderthal introgressed variant-containing enhancer experimental_58308 [Gene]
  • LOC132088842:Neanderthal introgressed variant-containing enhancer experimental_58341 [Gene]
  • LOC132088843:Neanderthal introgressed variant-containing enhancer experimental_58378 [Gene]
  • LOC132088844:Neanderthal introgressed variant-containing enhancer experimental_58486 [Gene]
  • LOC132088846:Neanderthal introgressed variant-containing enhancer experimental_58516 [Gene]
  • LOC126806103:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:1421072-1422271 [Gene]
  • LOC126806105:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:2530602-2531801 [Gene]
  • LOC126806097:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:602328-603527 [Gene]
  • RNASEH1-DT:RNASEH1 divergent transcript [Gene - HGNC]
  • 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]
  • LOC114004371:Sharpr-MPRA regulatory region 3808 [Gene]
  • LOC121725077:Sharpr-MPRA regulatory region 8446 [Gene]
  • TMEM18-DT:TMEM18 divergent transcript [Gene - HGNC]
  • TRAPPC12-AS1:TRAPPC12 antisense RNA 1 [Gene - HGNC]
  • LOC110121085:VISTA enhancer hs1385 [Gene]
  • ACP1:acid phosphatase 1 [Gene - OMIM - HGNC]
  • ADI1:acireductone dioxygenase 1 [Gene - OMIM - HGNC]
  • ALLC:allantoicase [Gene - OMIM - HGNC]
  • COLEC11:collectin subfamily member 11 [Gene - OMIM - HGNC]
  • DCDC2C:doublecortin domain containing 2C [Gene - HGNC]
  • FAM110C:family with sequence similarity 110 member C [Gene - OMIM - HGNC]
  • LINC01115:long intergenic non-protein coding RNA 1115 [Gene - HGNC]
  • LINC01249:long intergenic non-protein coding RNA 1249 [Gene - HGNC]
  • LINC01250:long intergenic non-protein coding RNA 1250 [Gene - HGNC]
  • LINC01304:long intergenic non-protein coding RNA 1304 [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]
  • MYT1L:myelin transcription factor 1 like [Gene - OMIM - HGNC]
  • PXDN:peroxidasin [Gene - OMIM - HGNC]
  • RNASEH1:ribonuclease H1 [Gene - OMIM - HGNC]
  • RPS7:ribosomal protein S7 [Gene - OMIM - HGNC]
  • SNTG2:syntrophin gamma 2 [Gene - OMIM - HGNC]
  • TPO:thyroid peroxidase [Gene - OMIM - HGNC]
  • TRAPPC12:trafficking protein particle complex subunit 12 [Gene - OMIM - HGNC]
  • TMEM18:transmembrane protein 18 [Gene - OMIM - HGNC]
  • LOC100996637:uncharacterized LOC100996637 [Gene]
  • LOC102723730:uncharacterized LOC102723730 [Gene]
  • LOC105373346:uncharacterized LOC105373346 [Gene]
  • LOC105373352:uncharacterized LOC105373352 [Gene]
  • LOC105373390:uncharacterized LOC105373390 [Gene]
  • LOC105373394:uncharacterized LOC105373394 [Gene]
Variant type:
copy number gain
Cytogenetic location:
2p25.3-25.2
Genomic location:
Preferred name:
GRCh38/hg38 2p25.3-25.2(chr2:30341-4642399)x3
HGVS:
  • NC_000002.12:g.(?_30341)_(4642399_?)dup
  • NC_000002.10:g.(?_20341)_(4667864_?)dup
  • NC_000002.11:g.(?_30341)_(4689989_?)dup
Links:
dbVar: nssv582360; dbVar: nsv534352
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
SCV000177128ISCA site 2

See additional submitters

no assertion criteria provided
Pathogenic
(Sep 16, 2011) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not 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 2, SCV000177128.3

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

Last Updated: May 7, 2024