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GRCh38/hg38 3p26.3-25.3(chr3:20213-9362037)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 10, 2014
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:
RCV000142284.6

Allele description [Variation Report for GRCh38/hg38 3p26.3-25.3(chr3:20213-9362037)x1]

GRCh38/hg38 3p26.3-25.3(chr3:20213-9362037)x1

Genes:
  • ARL8B:ADP ribosylation factor like GTPase 8B [Gene - OMIM - HGNC]
  • LOC129936036:ATAC-STARR-seq lymphoblastoid active region 19334 [Gene]
  • LOC129936037:ATAC-STARR-seq lymphoblastoid active region 19335 [Gene]
  • LOC129936038:ATAC-STARR-seq lymphoblastoid active region 19336 [Gene]
  • LOC129936039:ATAC-STARR-seq lymphoblastoid active region 19337 [Gene]
  • LOC129936040:ATAC-STARR-seq lymphoblastoid active region 19338 [Gene]
  • LOC129936041:ATAC-STARR-seq lymphoblastoid active region 19339 [Gene]
  • LOC129936042:ATAC-STARR-seq lymphoblastoid active region 19340 [Gene]
  • LOC129936043:ATAC-STARR-seq lymphoblastoid active region 19342 [Gene]
  • LOC129936046:ATAC-STARR-seq lymphoblastoid active region 19343 [Gene]
  • LOC129936049:ATAC-STARR-seq lymphoblastoid active region 19345 [Gene]
  • LOC129936053:ATAC-STARR-seq lymphoblastoid active region 19346 [Gene]
  • LOC129936055:ATAC-STARR-seq lymphoblastoid active region 19347 [Gene]
  • LOC129936057:ATAC-STARR-seq lymphoblastoid active region 19348 [Gene]
  • LOC129936060:ATAC-STARR-seq lymphoblastoid active region 19349 [Gene]
  • LOC129936061:ATAC-STARR-seq lymphoblastoid active region 19350 [Gene]
  • LOC129936062:ATAC-STARR-seq lymphoblastoid active region 19351 [Gene]
  • LOC129936063:ATAC-STARR-seq lymphoblastoid active region 19352 [Gene]
  • LOC129936064:ATAC-STARR-seq lymphoblastoid active region 19353 [Gene]
  • LOC129936065:ATAC-STARR-seq lymphoblastoid active region 19354 [Gene]
  • LOC129936066:ATAC-STARR-seq lymphoblastoid active region 19355 [Gene]
  • LOC129936067:ATAC-STARR-seq lymphoblastoid active region 19356 [Gene]
  • LOC129936068:ATAC-STARR-seq lymphoblastoid active region 19357 [Gene]
  • LOC129936069:ATAC-STARR-seq lymphoblastoid active region 19358 [Gene]
  • LOC129936070:ATAC-STARR-seq lymphoblastoid active region 19359 [Gene]
  • LOC129936071:ATAC-STARR-seq lymphoblastoid active region 19360 [Gene]
  • LOC129936073:ATAC-STARR-seq lymphoblastoid active region 19362 [Gene]
  • LOC129936074:ATAC-STARR-seq lymphoblastoid active region 19363 [Gene]
  • LOC129936075:ATAC-STARR-seq lymphoblastoid active region 19364 [Gene]
  • LOC129936076:ATAC-STARR-seq lymphoblastoid active region 19365 [Gene]
  • LOC129936079:ATAC-STARR-seq lymphoblastoid active region 19366 [Gene]
  • LOC129936080:ATAC-STARR-seq lymphoblastoid active region 19368 [Gene]
  • LOC129936081:ATAC-STARR-seq lymphoblastoid active region 19369 [Gene]
  • LOC129936082:ATAC-STARR-seq lymphoblastoid active region 19370 [Gene]
  • LOC129936083:ATAC-STARR-seq lymphoblastoid active region 19371 [Gene]
  • LOC129936084:ATAC-STARR-seq lymphoblastoid active region 19372 [Gene]
  • LOC129936086:ATAC-STARR-seq lymphoblastoid active region 19373 [Gene]
  • LOC129936087:ATAC-STARR-seq lymphoblastoid active region 19375 [Gene]
  • LOC129936089:ATAC-STARR-seq lymphoblastoid active region 19376 [Gene]
  • LOC129936090:ATAC-STARR-seq lymphoblastoid active region 19377 [Gene]
  • LOC129936091:ATAC-STARR-seq lymphoblastoid active region 19378 [Gene]
  • LOC129936092:ATAC-STARR-seq lymphoblastoid active region 19379 [Gene]
  • LOC129936096:ATAC-STARR-seq lymphoblastoid active region 19380 [Gene]
  • LOC129936098:ATAC-STARR-seq lymphoblastoid active region 19381 [Gene]
  • LOC129936099:ATAC-STARR-seq lymphoblastoid active region 19382 [Gene]
  • LOC129936100:ATAC-STARR-seq lymphoblastoid active region 19383 [Gene]
  • LOC129936101:ATAC-STARR-seq lymphoblastoid active region 19384 [Gene]
  • LOC129936102:ATAC-STARR-seq lymphoblastoid active region 19385 [Gene]
  • LOC129936103:ATAC-STARR-seq lymphoblastoid active region 19386 [Gene]
  • LOC129936104:ATAC-STARR-seq lymphoblastoid active region 19387 [Gene]
  • LOC129936105:ATAC-STARR-seq lymphoblastoid active region 19388 [Gene]
  • LOC129936106:ATAC-STARR-seq lymphoblastoid active region 19389 [Gene]
  • LOC129936107:ATAC-STARR-seq lymphoblastoid active region 19390 [Gene]
  • LOC129936108:ATAC-STARR-seq lymphoblastoid active region 19391 [Gene]
  • LOC129936109:ATAC-STARR-seq lymphoblastoid active region 19392 [Gene]
  • LOC129936110:ATAC-STARR-seq lymphoblastoid active region 19393 [Gene]
  • LOC129936113:ATAC-STARR-seq lymphoblastoid active region 19394 [Gene]
  • 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]
  • LOC129936035:ATAC-STARR-seq lymphoblastoid silent region 14006 [Gene]
  • LOC129936044:ATAC-STARR-seq lymphoblastoid silent region 14007 [Gene]
  • LOC129936045:ATAC-STARR-seq lymphoblastoid silent region 14008 [Gene]
  • LOC129936047:ATAC-STARR-seq lymphoblastoid silent region 14009 [Gene]
  • LOC129936048:ATAC-STARR-seq lymphoblastoid silent region 14010 [Gene]
  • LOC129936050:ATAC-STARR-seq lymphoblastoid silent region 14011 [Gene]
  • LOC129936051:ATAC-STARR-seq lymphoblastoid silent region 14012 [Gene]
  • LOC129936052:ATAC-STARR-seq lymphoblastoid silent region 14013 [Gene]
  • LOC129936054:ATAC-STARR-seq lymphoblastoid silent region 14015 [Gene]
  • LOC129936056:ATAC-STARR-seq lymphoblastoid silent region 14016 [Gene]
  • LOC129936058:ATAC-STARR-seq lymphoblastoid silent region 14017 [Gene]
  • LOC129936059:ATAC-STARR-seq lymphoblastoid silent region 14018 [Gene]
  • LOC129936072:ATAC-STARR-seq lymphoblastoid silent region 14019 [Gene]
  • LOC129936077:ATAC-STARR-seq lymphoblastoid silent region 14020 [Gene]
  • LOC129936078:ATAC-STARR-seq lymphoblastoid silent region 14021 [Gene]
  • LOC129936085:ATAC-STARR-seq lymphoblastoid silent region 14022 [Gene]
  • LOC129936088:ATAC-STARR-seq lymphoblastoid silent region 14023 [Gene]
  • LOC129936093:ATAC-STARR-seq lymphoblastoid silent region 14024 [Gene]
  • LOC129936094:ATAC-STARR-seq lymphoblastoid silent region 14025 [Gene]
  • LOC129936095:ATAC-STARR-seq lymphoblastoid silent region 14026 [Gene]
  • LOC129936097:ATAC-STARR-seq lymphoblastoid silent region 14027 [Gene]
  • LOC129936111:ATAC-STARR-seq lymphoblastoid silent region 14028 [Gene]
  • LOC129936112:ATAC-STARR-seq lymphoblastoid silent region 14029 [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]
  • BHLHE40-AS1:BHLHE40 antisense RNA 1 [Gene - HGNC]
  • LOC126806587:BRD4-independent group 4 enhancer GRCh37_chr3:1277185-1278384 [Gene]
  • LOC126806588:BRD4-independent group 4 enhancer GRCh37_chr3:3079797-3080996 [Gene]
  • LOC126806594:BRD4-independent group 4 enhancer GRCh37_chr3:5605144-5606343 [Gene]
  • LOC126806585:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:118683-119882 [Gene]
  • LOC126806595:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:5740332-5741531 [Gene]
  • LOC126806596:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:6531900-6533099 [Gene]
  • LOC126806598:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:8361398-8362597 [Gene]
  • CHL1-AS1:CHL1 antisense RNA 1 [Gene - HGNC]
  • CHL1-AS2:CHL1 antisense RNA 2 [Gene - HGNC]
  • CNTN4-AS1:CNTN4 antisense RNA 1 [Gene - HGNC]
  • CNTN4-AS2:CNTN4 antisense RNA 2 [Gene - HGNC]
  • LOC115995504:CRISPRi-validated cis-regulatory element chr3.91 [Gene]
  • EDEM1:ER degradation enhancing alpha-mannosidase like protein 1 [Gene - OMIM - HGNC]
  • LOC111429626:FOXA motif-containing MPRA enhancer 226 [Gene]
  • GRM7-AS1:GRM7 antisense RNA 1 [Gene - HGNC]
  • GRM7-AS2:GRM7 antisense RNA 2 [Gene - HGNC]
  • GRM7-AS3:GRM7 antisense RNA 3 [Gene - HGNC]
  • ITPR1-DT:ITPR1 divergent transcript [Gene - HGNC]
  • LMCD1:LIM and cysteine rich domains 1 [Gene - OMIM - HGNC]
  • LMCD1-AS1:LMCD1 antisense RNA 1 [Gene - HGNC]
  • LOC126806586:MED14-independent group 3 enhancer GRCh37_chr3:152955-154154 [Gene]
  • LOC126806589:MED14-independent group 3 enhancer GRCh37_chr3:3600748-3601947 [Gene]
  • LOC126806590:MED14-independent group 3 enhancer GRCh37_chr3:4855759-4856958 [Gene]
  • LOC111501788:MED14-independent group 3 enhancer GRCh37_chr3:5390480-5391679 [Gene]
  • LOC126806597:MED14-independent group 3 enhancer GRCh37_chr3:8082288-8083487 [Gene]
  • LOC129389017:MPRA-validated peak4526 silencer [Gene]
  • LOC129389018:MPRA-validated peak4528 silencer [Gene]
  • LOC129389019:MPRA-validated peak4531 silencer [Gene]
  • LOC132088944:Neanderthal introgressed variant-containing enhancer experimental_68491 [Gene]
  • LOC132088949:Neanderthal introgressed variant-containing enhancer experimental_68954 [Gene]
  • LOC132088954:Neanderthal introgressed variant-containing enhancer experimental_69430 [Gene]
  • LOC132088963:Neanderthal introgressed variant-containing enhancer experimental_69928 [Gene]
  • LOC132088964:Neanderthal introgressed variant-containing enhancer experimental_69934 [Gene]
  • LOC132088965:Neanderthal introgressed variant-containing enhancer experimental_69968 [Gene]
  • LOC132088977:Neanderthal introgressed variant-containing enhancer experimental_70950 [Gene]
  • LOC132088979:Neanderthal introgressed variant-containing enhancer experimental_71090 [Gene]
  • LOC132088980:Neanderthal introgressed variant-containing enhancer experimental_71094 [Gene]
  • LOC126806591:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5036716-5037915 [Gene]
  • LOC126806592:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5064405-5065604 [Gene]
  • LOC126806593:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5371861-5373060 [Gene]
  • LOC126806599:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:8911034-8912233 [Gene]
  • RAD18:RAD18 E3 ubiquitin protein ligase [Gene - OMIM - HGNC]
  • SETMAR:SET domain and mariner transposase fusion gene [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]
  • LOC122889024:Sharpr-MPRA regulatory region 1018 [Gene]
  • LOC122889018:Sharpr-MPRA regulatory region 107 [Gene]
  • LOC121009636:Sharpr-MPRA regulatory region 12048 [Gene]
  • LOC122889020:Sharpr-MPRA regulatory region 12228 [Gene]
  • LOC122889019:Sharpr-MPRA regulatory region 14120 [Gene]
  • LOC112935932:Sharpr-MPRA regulatory region 14798 [Gene]
  • LOC121009637:Sharpr-MPRA regulatory region 2381 [Gene]
  • LOC122889026:Sharpr-MPRA regulatory region 3594 [Gene]
  • LOC122889025:Sharpr-MPRA regulatory region 4351 [Gene]
  • LOC112935931:Sharpr-MPRA regulatory region 4455 [Gene]
  • LOC122889023:Sharpr-MPRA regulatory region 5493 [Gene]
  • LOC122889022:Sharpr-MPRA regulatory region 5688 [Gene]
  • LOC121725127:Sharpr-MPRA regulatory region 6601 [Gene]
  • LOC122889021:Sharpr-MPRA regulatory region 7157 [Gene]
  • LOC122889017:Sharpr-MPRA regulatory region 9777 [Gene]
  • BHLHE40:basic helix-loop-helix family member e40 [Gene - OMIM - HGNC]
  • CAV3:caveolin 3 [Gene - OMIM - HGNC]
  • CHL1:cell adhesion molecule L1 like [Gene - OMIM - HGNC]
  • CRBN:cereblon [Gene - OMIM - HGNC]
  • CNTN4:contactin 4 [Gene - OMIM - HGNC]
  • CNTN6:contactin 6 [Gene - OMIM - HGNC]
  • EGOT:eosinophil granule ontogeny transcript [Gene - OMIM - HGNC]
  • GRM7:glutamate metabotropic receptor 7 [Gene - OMIM - HGNC]
  • ITPR1:inositol 1,4,5-trisphosphate receptor type 1 [Gene - OMIM - HGNC]
  • IL5RA:interleukin 5 receptor subunit alpha [Gene - OMIM - HGNC]
  • LRRN1:leucine rich repeat neuronal 1 [Gene - OMIM - HGNC]
  • LINC01266:long intergenic non-protein coding RNA 1266 [Gene - HGNC]
  • LINC01986:long intergenic non-protein coding RNA 1986 [Gene - HGNC]
  • LINC00312:long intergenic non-protein coding RNA 312 [Gene - OMIM - HGNC]
  • LOC107522035:meiotic recombination hotspot S [Gene]
  • LOC107522028:meiotic recombination hotspot T [Gene]
  • MIR4790:microRNA 4790 [Gene - HGNC]
  • OXTR:oxytocin receptor [Gene - OMIM - HGNC]
  • SSUH2:ssu-2 homolog [Gene - OMIM - HGNC]
  • SUMF1:sulfatase modifying factor 1 [Gene - OMIM - HGNC]
  • TRNT1:tRNA nucleotidyl transferase 1 [Gene - OMIM - HGNC]
  • LOC100130207:uncharacterized LOC100130207 [Gene]
  • LOC101927394:uncharacterized LOC101927394 [Gene]
  • LOC105376944:uncharacterized LOC105376944 [Gene]
Variant type:
copy number loss
Cytogenetic location:
3p26.3-25.3
Genomic location:
Preferred name:
GRCh38/hg38 3p26.3-25.3(chr3:20213-9362037)x1
HGVS:
  • NC_000003.12:g.(?_20213)_(9362037_?)del
  • NC_000003.10:g.(?_36891)_(9378721_?)del
  • NC_000003.11:g.(?_61891)_(9403721_?)del
Links:
dbVar: nssv3395351; dbVar: nsv996168
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
SCV000183598ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Mar 10, 2014) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
humannot providedyes1not 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 1, SCV000183598.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1human1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024