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GRCh38/hg38 3p25.3(chr3:9393349-9956171)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:
RCV000051481.5

Allele description [Variation Report for GRCh38/hg38 3p25.3(chr3:9393349-9956171)x1]

GRCh38/hg38 3p25.3(chr3:9393349-9956171)x1

Genes:
  • LOC107303337:3p25 PRRT3 Alu-mediated recombination region [Gene]
  • OGG1:8-oxoguanine DNA glycosylase [Gene - OMIM - HGNC]
  • ARPC4-TTLL3:ARPC4-TTLL3 readthrough [Gene - HGNC]
  • LOC129936126:ATAC-STARR-seq lymphoblastoid active region 19403 [Gene]
  • LOC129936128:ATAC-STARR-seq lymphoblastoid active region 19405 [Gene]
  • LOC129936131:ATAC-STARR-seq lymphoblastoid active region 19406 [Gene]
  • LOC129936132:ATAC-STARR-seq lymphoblastoid active region 19407 [Gene]
  • LOC129936136:ATAC-STARR-seq lymphoblastoid active region 19409 [Gene]
  • LOC129936137:ATAC-STARR-seq lymphoblastoid active region 19410 [Gene]
  • LOC129936139:ATAC-STARR-seq lymphoblastoid active region 19411 [Gene]
  • LOC129936145:ATAC-STARR-seq lymphoblastoid active region 19413 [Gene]
  • LOC129936125:ATAC-STARR-seq lymphoblastoid silent region 14033 [Gene]
  • LOC129936127:ATAC-STARR-seq lymphoblastoid silent region 14034 [Gene]
  • LOC129936129:ATAC-STARR-seq lymphoblastoid silent region 14038 [Gene]
  • LOC129936130:ATAC-STARR-seq lymphoblastoid silent region 14039 [Gene]
  • LOC129936133:ATAC-STARR-seq lymphoblastoid silent region 14040 [Gene]
  • LOC129936134:ATAC-STARR-seq lymphoblastoid silent region 14041 [Gene]
  • LOC129936135:ATAC-STARR-seq lymphoblastoid silent region 14042 [Gene]
  • LOC129936138:ATAC-STARR-seq lymphoblastoid silent region 14044 [Gene]
  • LOC129936140:ATAC-STARR-seq lymphoblastoid silent region 14047 [Gene]
  • LOC129936141:ATAC-STARR-seq lymphoblastoid silent region 14048 [Gene]
  • LOC129936142:ATAC-STARR-seq lymphoblastoid silent region 14049 [Gene]
  • LOC129936143:ATAC-STARR-seq lymphoblastoid silent region 14050 [Gene]
  • LOC129936144:ATAC-STARR-seq lymphoblastoid silent region 14051 [Gene]
  • LOC129936146:ATAC-STARR-seq lymphoblastoid silent region 14052 [Gene]
  • LHFPL4:LHFPL tetraspan subfamily member 4 [Gene - OMIM - HGNC]
  • LOC129389020:MPRA-validated peak4533 silencer [Gene]
  • PRRT3-AS1:PRRT3 antisense RNA 1 [Gene - OMIM - HGNC]
  • RPUSD3:RNA pseudouridine synthase D3 [Gene - OMIM - HGNC]
  • SETD5:SET domain containing 5 [Gene - OMIM - HGNC]
  • LOC122889027:Sharpr-MPRA regulatory region 11896 [Gene]
  • LOC122889029:Sharpr-MPRA regulatory region 13942 [Gene]
  • LOC112935963:Sharpr-MPRA regulatory region 14744 [Gene]
  • LOC122889028:Sharpr-MPRA regulatory region 15302 [Gene]
  • LOC121009638:Sharpr-MPRA regulatory region 4794 [Gene]
  • LOC122889030:Sharpr-MPRA regulatory region 9891 [Gene]
  • THUMPD3-AS1:THUMPD3 antisense RNA 1 [Gene - HGNC]
  • ARPC4:actin related protein 2/3 complex subunit 4 [Gene - OMIM - HGNC]
  • BRPF1:bromodomain and PHD finger containing 1 [Gene - OMIM - HGNC]
  • CAMK1:calcium/calmodulin dependent protein kinase I [Gene - OMIM - HGNC]
  • CIDEC:cell death inducing DFFA like effector c [Gene - OMIM - HGNC]
  • CPNE9:copine family member 9 [Gene - HGNC]
  • CRELD1:cysteine rich with EGF like domains 1 [Gene - OMIM - HGNC]
  • IL17RC:interleukin 17 receptor C [Gene - OMIM - HGNC]
  • IL17RE:interleukin 17 receptor E [Gene - OMIM - HGNC]
  • JAGN1:jagunal homolog 1 [Gene - OMIM - HGNC]
  • MTMR14:myotubularin related protein 14 [Gene - OMIM - HGNC]
  • PRRT3:proline rich transmembrane protein 3 [Gene - OMIM - HGNC]
  • TADA3:transcriptional adaptor 3 [Gene - OMIM - HGNC]
  • TTLL3:tubulin tyrosine ligase like 3 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
GRCh38/hg38 3p25.3(chr3:9393349-9956171)x1
HGVS:
  • NC_000003.12:g.(?_9393349)_(9956171_?)del
  • NC_000003.10:g.(?_9410033)_(9972855_?)del
  • NC_000003.11:g.(?_9435033)_(9997855_?)del
Links:
dbVar: nssv577894; dbVar: nsv530003
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
SCV000078829GeneDx
criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		not providedclinical 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

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, SCV000078829.5

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

Last Updated: Oct 14, 2023