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GRCh38/hg38 2p25.3(chr2:50661-3293835)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 12, 2011
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000053977.5

Allele description [Variation Report for GRCh38/hg38 2p25.3(chr2:50661-3293835)x1]

GRCh38/hg38 2p25.3(chr2:50661-3293835)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]
  • 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]
  • 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]
  • 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]
  • 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]
  • LOC129388816:MPRA-validated peak3584 silencer [Gene]
  • MYT1L-AS1:MYT1L antisense RNA 1 [Gene - HGNC]
  • LOC132088839:Neanderthal introgressed variant-containing enhancer experimental_58239 [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]
  • 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]
  • LOC110121085:VISTA enhancer hs1385 [Gene]
  • ACP1:acid phosphatase 1 [Gene - OMIM - HGNC]
  • LINC01115:long intergenic non-protein coding RNA 1115 [Gene - HGNC]
  • LINC01250:long intergenic non-protein coding RNA 1250 [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]
  • SNTG2:syntrophin gamma 2 [Gene - OMIM - HGNC]
  • TPO:thyroid peroxidase [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]
Variant type:
copy number loss
Cytogenetic location:
2p25.3
Genomic location:
Preferred name:
GRCh38/hg38 2p25.3(chr2:50661-3293835)x1
HGVS:
  • NC_000002.12:g.(?_50661)_(3293835_?)del
  • NC_000002.10:g.(?_40661)_(3276613_?)del
  • NC_000002.11:g.(?_50661)_(3297606_?)del
Links:
dbVar: nssv577683; dbVar: nsv532645
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
SCV000081340GeneDx
criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 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

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]
PMID:
21844811
PMCID:
PMC3661946

Details of each submission

From GeneDx, SCV000081340.4

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

Last Updated: Sep 1, 2024