GRCh38/hg38 3p25.3(chr3:8812036-9953438)x3 AND See cases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 8, 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:: RCV000137329.5

Allele description [Variation Report for GRCh38/hg38 3p25.3(chr3:8812036-9953438)x3]

GRCh38/hg38 3p25.3(chr3:8812036-9953438)x3

Genes:

LOC107303337:3p25 PRRT3 Alu-mediated recombination region [Gene]
OGG1:8-oxoguanine DNA glycosylase [Gene - OMIM - HGNC]
ARPC4-TTLL3:ARPC4-TTLL3 readthrough [Gene - HGNC]
LOC129936114:ATAC-STARR-seq lymphoblastoid active region 19395 [Gene]
LOC129936115:ATAC-STARR-seq lymphoblastoid active region 19396 [Gene]
LOC129936118:ATAC-STARR-seq lymphoblastoid active region 19397 [Gene]
LOC129936119:ATAC-STARR-seq lymphoblastoid active region 19398 [Gene]
LOC129936121:ATAC-STARR-seq lymphoblastoid active region 19399 [Gene]
LOC129936122:ATAC-STARR-seq lymphoblastoid active region 19400 [Gene]
LOC129936123:ATAC-STARR-seq lymphoblastoid active region 19401 [Gene]
LOC129936124:ATAC-STARR-seq lymphoblastoid active region 19402 [Gene]
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]
LOC129936116:ATAC-STARR-seq lymphoblastoid silent region 14030 [Gene]
LOC129936117:ATAC-STARR-seq lymphoblastoid silent region 14031 [Gene]
LOC129936120:ATAC-STARR-seq lymphoblastoid silent region 14032 [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]
LOC126806599:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:8911034-8912233 [Gene]
PRRT3-AS1:PRRT3 antisense RNA 1 [Gene - OMIM - HGNC]
RAD18:RAD18 E3 ubiquitin protein ligase [Gene - OMIM - HGNC]
RPUSD3:RNA pseudouridine synthase D3 [Gene - OMIM - HGNC]
SETD5:SET domain containing 5 [Gene - OMIM - HGNC]
SRGAP3:SLIT-ROBO Rho GTPase activating protein 3 [Gene - OMIM - HGNC]
SRGAP3-AS2:SRGAP3 antisense RNA 2 [Gene - HGNC]
SRGAP3-AS3:SRGAP3 antisense RNA 3 [Gene - HGNC]
SRGAP3-AS4:SRGAP3 antisense RNA 4 [Gene - 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]
LOC122889026:Sharpr-MPRA regulatory region 3594 [Gene]
LOC122889025:Sharpr-MPRA regulatory region 4351 [Gene]
LOC121009638:Sharpr-MPRA regulatory region 4794 [Gene]
LOC122889030:Sharpr-MPRA regulatory region 9891 [Gene]
THUMPD3:THUMP domain containing 3 [Gene - HGNC]
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 gain

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

GRCh38/hg38 3p25.3(chr3:8812036-9953438)x3

HGVS:

NC_000003.12:g.(?_8812036)_(9953438_?)dup
NC_000003.10:g.(?_8828722)_(9970122_?)dup
NC_000003.11:g.(?_8853722)_(9995122_?)dup

Links:

dbVar: nssv1415132; dbVar: nsv817255

Observations:

Condition(s)

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

Recent activity

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Homo sapiens chromosome 20 genomic scaffold, GRCh38.p14 Primary Assembly HSCHR20...
Homo sapiens chromosome 20 genomic scaffold, GRCh38.p14 Primary Assembly HSCHR20_CTG2
gi|568802081|gnl|ASM:GCF_000001305. CHR20_CTG2|ref|NT_011362.11||gpp|GPS_003205661.1|

Nucleotide
Trachyglanis cf. ineac ZSM 39343 bio-material ZSM:DRC-2009/0794 cytochrome b (Cy...
Trachyglanis cf. ineac ZSM 39343 bio-material ZSM:DRC-2009/0794 cytochrome b (Cytb) gene, partial cds; mitochondrial
gi|723451316|gb|KC331898.1|

Nucleotide
Homo sapiens zinc finger protein 256, mRNA (cDNA clone MGC:1413 IMAGE:3138611), ...
Homo sapiens zinc finger protein 256, mRNA (cDNA clone MGC:1413 IMAGE:3138611), complete cds
gi|12655164|gb|BC001438.1|

Nucleotide
Reduced procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 activity in cultured f...
Reduced procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 activity in cultured fibroblasts

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000177548	ISCA site 1 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Uncertain significance (Apr 8, 2011)	unknown	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

SCV000177548

ISCA site 1

See additional submitters

no assertion criteria provided

Uncertain significance
(Apr 8, 2011)

unknown

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

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 1, SCV000177548.4

#	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	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

ClinVar

Relating variation to medicine