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:

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

Recent activity

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Influenza A virus (A/poultry/Italy/330/1997(H5N2)) segment 7, complete sequence
Influenza A virus (A/poultry/Italy/330/1997(H5N2)) segment 7, complete sequence
gi|118313946|gnl|NIGSP|NIGSP-IT-000 |gb|CY017404.1|

Nucleotide
Ssq sasquatch [Mus musculus]
Ssq sasquatch [Mus musculus]
Gene ID:109577

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000078829	GeneDx	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	not provided	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000078829

GeneDx

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))

Pathogenic
(Aug 12, 2011)

not provided

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	not provided	yes	1	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: Oct 14, 2023

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Relating variation to medicine