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GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 17, 2012
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:
RCV000140814.4

Allele description

GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1

Genes:
  • HACD2:3-hydroxyacyl-CoA dehydratase 2 [Gene - OMIM - HGNC]
  • ALDH1L1-AS1:ALDH1L1 and SLC41A3 antisense RNA 1 [Gene - HGNC]
  • ALDH1L1-AS2:ALDH1L1 antisense RNA 2 [Gene - HGNC]
  • LOC129937352:ATAC-STARR-seq lymphoblastoid active region 20350 [Gene]
  • LOC129937353:ATAC-STARR-seq lymphoblastoid active region 20351 [Gene]
  • LOC129937354:ATAC-STARR-seq lymphoblastoid active region 20352 [Gene]
  • LOC129937355:ATAC-STARR-seq lymphoblastoid active region 20353 [Gene]
  • LOC129937356:ATAC-STARR-seq lymphoblastoid active region 20354 [Gene]
  • LOC129937358:ATAC-STARR-seq lymphoblastoid active region 20355 [Gene]
  • LOC129937359:ATAC-STARR-seq lymphoblastoid active region 20356 [Gene]
  • LOC129937360:ATAC-STARR-seq lymphoblastoid active region 20357 [Gene]
  • LOC129937361:ATAC-STARR-seq lymphoblastoid active region 20358 [Gene]
  • LOC129937362:ATAC-STARR-seq lymphoblastoid active region 20359 [Gene]
  • LOC129937363:ATAC-STARR-seq lymphoblastoid active region 20360 [Gene]
  • LOC129937364:ATAC-STARR-seq lymphoblastoid active region 20361 [Gene]
  • LOC129937365:ATAC-STARR-seq lymphoblastoid active region 20362 [Gene]
  • LOC129937366:ATAC-STARR-seq lymphoblastoid active region 20363 [Gene]
  • LOC129937367:ATAC-STARR-seq lymphoblastoid active region 20364 [Gene]
  • LOC129937369:ATAC-STARR-seq lymphoblastoid active region 20365 [Gene]
  • LOC129937370:ATAC-STARR-seq lymphoblastoid active region 20366 [Gene]
  • LOC129937371:ATAC-STARR-seq lymphoblastoid active region 20368 [Gene]
  • LOC129937372:ATAC-STARR-seq lymphoblastoid active region 20369 [Gene]
  • LOC129937373:ATAC-STARR-seq lymphoblastoid active region 20373 [Gene]
  • LOC129937374:ATAC-STARR-seq lymphoblastoid active region 20374 [Gene]
  • LOC129937375:ATAC-STARR-seq lymphoblastoid active region 20375 [Gene]
  • LOC129937376:ATAC-STARR-seq lymphoblastoid active region 20376 [Gene]
  • LOC129937379:ATAC-STARR-seq lymphoblastoid active region 20377 [Gene]
  • LOC129937380:ATAC-STARR-seq lymphoblastoid active region 20378 [Gene]
  • LOC129937381:ATAC-STARR-seq lymphoblastoid active region 20379 [Gene]
  • LOC129937383:ATAC-STARR-seq lymphoblastoid active region 20380 [Gene]
  • LOC129937384:ATAC-STARR-seq lymphoblastoid active region 20382 [Gene]
  • LOC129937386:ATAC-STARR-seq lymphoblastoid active region 20384 [Gene]
  • LOC129937387:ATAC-STARR-seq lymphoblastoid active region 20385 [Gene]
  • LOC129937388:ATAC-STARR-seq lymphoblastoid active region 20386 [Gene]
  • LOC129937390:ATAC-STARR-seq lymphoblastoid active region 20387 [Gene]
  • LOC129937391:ATAC-STARR-seq lymphoblastoid active region 20389 [Gene]
  • LOC129937393:ATAC-STARR-seq lymphoblastoid active region 20390 [Gene]
  • LOC129937394:ATAC-STARR-seq lymphoblastoid active region 20391 [Gene]
  • LOC129937395:ATAC-STARR-seq lymphoblastoid active region 20392 [Gene]
  • LOC129937399:ATAC-STARR-seq lymphoblastoid active region 20393 [Gene]
  • LOC129937400:ATAC-STARR-seq lymphoblastoid active region 20394 [Gene]
  • LOC129937403:ATAC-STARR-seq lymphoblastoid active region 20395 [Gene]
  • LOC129937405:ATAC-STARR-seq lymphoblastoid active region 20396 [Gene]
  • LOC129937407:ATAC-STARR-seq lymphoblastoid active region 20397 [Gene]
  • LOC129937408:ATAC-STARR-seq lymphoblastoid active region 20398 [Gene]
  • LOC129937409:ATAC-STARR-seq lymphoblastoid active region 20399 [Gene]
  • LOC129937410:ATAC-STARR-seq lymphoblastoid active region 20400 [Gene]
  • LOC129937411:ATAC-STARR-seq lymphoblastoid active region 20401 [Gene]
  • LOC129937413:ATAC-STARR-seq lymphoblastoid active region 20403 [Gene]
  • LOC129937414:ATAC-STARR-seq lymphoblastoid active region 20404 [Gene]
  • LOC129937415:ATAC-STARR-seq lymphoblastoid active region 20405 [Gene]
  • LOC129937416:ATAC-STARR-seq lymphoblastoid active region 20406 [Gene]
  • LOC129937417:ATAC-STARR-seq lymphoblastoid active region 20407 [Gene]
  • LOC129937420:ATAC-STARR-seq lymphoblastoid active region 20408 [Gene]
  • LOC129937425:ATAC-STARR-seq lymphoblastoid active region 20409 [Gene]
  • LOC129937426:ATAC-STARR-seq lymphoblastoid active region 20412 [Gene]
  • LOC129937427:ATAC-STARR-seq lymphoblastoid active region 20413 [Gene]
  • LOC129937428:ATAC-STARR-seq lymphoblastoid active region 20414 [Gene]
  • LOC129937429:ATAC-STARR-seq lymphoblastoid active region 20415 [Gene]
  • LOC129937430:ATAC-STARR-seq lymphoblastoid active region 20416 [Gene]
  • LOC129937431:ATAC-STARR-seq lymphoblastoid active region 20417 [Gene]
  • LOC129937432:ATAC-STARR-seq lymphoblastoid active region 20418 [Gene]
  • LOC129937434:ATAC-STARR-seq lymphoblastoid active region 20421 [Gene]
  • LOC129937435:ATAC-STARR-seq lymphoblastoid active region 20422 [Gene]
  • LOC129937436:ATAC-STARR-seq lymphoblastoid active region 20423 [Gene]
  • LOC129937437:ATAC-STARR-seq lymphoblastoid active region 20424 [Gene]
  • LOC129937438:ATAC-STARR-seq lymphoblastoid active region 20425 [Gene]
  • LOC129937440:ATAC-STARR-seq lymphoblastoid active region 20426 [Gene]
  • LOC129937441:ATAC-STARR-seq lymphoblastoid active region 20427 [Gene]
  • LOC129937445:ATAC-STARR-seq lymphoblastoid active region 20428 [Gene]
  • LOC129937446:ATAC-STARR-seq lymphoblastoid active region 20429 [Gene]
  • LOC129937447:ATAC-STARR-seq lymphoblastoid active region 20430 [Gene]
  • LOC129937449:ATAC-STARR-seq lymphoblastoid active region 20431 [Gene]
  • LOC129937450:ATAC-STARR-seq lymphoblastoid active region 20432 [Gene]
  • LOC129937451:ATAC-STARR-seq lymphoblastoid active region 20433 [Gene]
  • LOC129937453:ATAC-STARR-seq lymphoblastoid active region 20434 [Gene]
  • LOC129937458:ATAC-STARR-seq lymphoblastoid active region 20435 [Gene]
  • LOC129937459:ATAC-STARR-seq lymphoblastoid active region 20436 [Gene]
  • LOC129937461:ATAC-STARR-seq lymphoblastoid active region 20437 [Gene]
  • LOC129937465:ATAC-STARR-seq lymphoblastoid active region 20439 [Gene]
  • LOC129937467:ATAC-STARR-seq lymphoblastoid active region 20441 [Gene]
  • LOC129937357:ATAC-STARR-seq lymphoblastoid silent region 14638 [Gene]
  • LOC129937368:ATAC-STARR-seq lymphoblastoid silent region 14639 [Gene]
  • LOC129937377:ATAC-STARR-seq lymphoblastoid silent region 14641 [Gene]
  • LOC129937378:ATAC-STARR-seq lymphoblastoid silent region 14642 [Gene]
  • LOC129937382:ATAC-STARR-seq lymphoblastoid silent region 14643 [Gene]
  • LOC129937385:ATAC-STARR-seq lymphoblastoid silent region 14644 [Gene]
  • LOC129937389:ATAC-STARR-seq lymphoblastoid silent region 14645 [Gene]
  • LOC129937392:ATAC-STARR-seq lymphoblastoid silent region 14646 [Gene]
  • LOC129937396:ATAC-STARR-seq lymphoblastoid silent region 14647 [Gene]
  • LOC129937397:ATAC-STARR-seq lymphoblastoid silent region 14648 [Gene]
  • LOC129937398:ATAC-STARR-seq lymphoblastoid silent region 14649 [Gene]
  • LOC129937401:ATAC-STARR-seq lymphoblastoid silent region 14650 [Gene]
  • LOC129937402:ATAC-STARR-seq lymphoblastoid silent region 14651 [Gene]
  • LOC129937404:ATAC-STARR-seq lymphoblastoid silent region 14652 [Gene]
  • LOC129937406:ATAC-STARR-seq lymphoblastoid silent region 14653 [Gene]
  • LOC129937412:ATAC-STARR-seq lymphoblastoid silent region 14654 [Gene]
  • LOC129937418:ATAC-STARR-seq lymphoblastoid silent region 14655 [Gene]
  • LOC129937419:ATAC-STARR-seq lymphoblastoid silent region 14656 [Gene]
  • LOC129937421:ATAC-STARR-seq lymphoblastoid silent region 14657 [Gene]
  • LOC129937422:ATAC-STARR-seq lymphoblastoid silent region 14658 [Gene]
  • LOC129937423:ATAC-STARR-seq lymphoblastoid silent region 14659 [Gene]
  • LOC129937424:ATAC-STARR-seq lymphoblastoid silent region 14660 [Gene]
  • LOC129937433:ATAC-STARR-seq lymphoblastoid silent region 14661 [Gene]
  • LOC129937439:ATAC-STARR-seq lymphoblastoid silent region 14662 [Gene]
  • LOC129937442:ATAC-STARR-seq lymphoblastoid silent region 14664 [Gene]
  • LOC129937443:ATAC-STARR-seq lymphoblastoid silent region 14665 [Gene]
  • LOC129937444:ATAC-STARR-seq lymphoblastoid silent region 14666 [Gene]
  • LOC129937448:ATAC-STARR-seq lymphoblastoid silent region 14667 [Gene]
  • LOC129937452:ATAC-STARR-seq lymphoblastoid silent region 14668 [Gene]
  • LOC129937454:ATAC-STARR-seq lymphoblastoid silent region 14669 [Gene]
  • LOC129937455:ATAC-STARR-seq lymphoblastoid silent region 14670 [Gene]
  • LOC129937456:ATAC-STARR-seq lymphoblastoid silent region 14672 [Gene]
  • LOC129937457:ATAC-STARR-seq lymphoblastoid silent region 14673 [Gene]
  • LOC129937460:ATAC-STARR-seq lymphoblastoid silent region 14674 [Gene]
  • LOC129937462:ATAC-STARR-seq lymphoblastoid silent region 14676 [Gene]
  • LOC129937463:ATAC-STARR-seq lymphoblastoid silent region 14677 [Gene]
  • LOC129937464:ATAC-STARR-seq lymphoblastoid silent region 14678 [Gene]
  • LOC129937466:ATAC-STARR-seq lymphoblastoid silent region 14679 [Gene]
  • LOC129937468:ATAC-STARR-seq lymphoblastoid silent region 14680 [Gene]
  • LOC126806793:BRD4-independent group 4 enhancer GRCh37_chr3:123966684-123967883 [Gene]
  • LOC126806794:BRD4-independent group 4 enhancer GRCh37_chr3:124128425-124129624 [Gene]
  • LOC126806801:BRD4-independent group 4 enhancer GRCh37_chr3:126207907-126209106 [Gene]
  • CD86:CD86 molecule [Gene - OMIM - HGNC]
  • LOC126806789:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:122353940-122355139 [Gene]
  • LOC126806792:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:123511339-123512538 [Gene]
  • LOC126806796:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:124229048-124230247 [Gene]
  • LOC126806799:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:125119796-125120995 [Gene]
  • CFAP100-DT:CFAP100 divergent transcript [Gene - HGNC]
  • LOC111562374:HNF1 motif-containing MPRA enhancer 180 [Gene]
  • LOC111365173:HNF4 motif-containing MPRA enhancer 1/2 [Gene]
  • HSPBAP1:HSPB1 associated protein 1 [Gene - OMIM - HGNC]
  • KLF15:KLF transcription factor 15 [Gene - OMIM - HGNC]
  • LOC126806788:MED14-independent group 3 enhancer GRCh37_chr3:122215008-122216207 [Gene]
  • LOC126806791:MED14-independent group 3 enhancer GRCh37_chr3:123347871-123349070 [Gene]
  • LOC126806795:MED14-independent group 3 enhancer GRCh37_chr3:124209527-124210726 [Gene]
  • LOC126806797:MED14-independent group 3 enhancer GRCh37_chr3:124720175-124721374 [Gene]
  • LOC126806800:MED14-independent group 3 enhancer GRCh37_chr3:125926972-125928171 [Gene]
  • LOC129389121:MPRA-validated peak4796 silencer [Gene]
  • LOC129389122:MPRA-validated peak4798 silencer [Gene]
  • LOC129389123:MPRA-validated peak4799 silencer [Gene]
  • LOC129389124:MPRA-validated peak4801 silencer [Gene]
  • LOC129389125:MPRA-validated peak4802 silencer [Gene]
  • LOC129389126:MPRA-validated peak4803 silencer [Gene]
  • LOC129389127:MPRA-validated peak4810 silencer [Gene]
  • LOC129389128:MPRA-validated peak4813 silencer [Gene]
  • MYLK-AS1:MYLK antisense RNA 1 [Gene - HGNC]
  • MYLK-AS2:MYLK antisense RNA 2 [Gene - HGNC]
  • LOC132088863:Neanderthal introgressed variant-containing enhancer experimental_64577 [Gene]
  • LOC126806790:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:122387501-122388700 [Gene]
  • LOC126806798:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:124950809-124952008 [Gene]
  • SEC22A:SEC22 homolog A, vesicle trafficking protein [Gene - OMIM - HGNC]
  • LOC112872294:Sharpr-MPRA regulatory region 10510 [Gene]
  • LOC121009685:Sharpr-MPRA regulatory region 10778 [Gene]
  • LOC123038168:Sharpr-MPRA regulatory region 1093 [Gene]
  • LOC123038164:Sharpr-MPRA regulatory region 1098 [Gene]
  • LOC123038162:Sharpr-MPRA regulatory region 13157 [Gene]
  • LOC123038167:Sharpr-MPRA regulatory region 13474 [Gene]
  • LOC112872295:Sharpr-MPRA regulatory region 1791 [Gene]
  • LOC112872296:Sharpr-MPRA regulatory region 2719 [Gene]
  • LOC121725154:Sharpr-MPRA regulatory region 5497 [Gene]
  • LOC112872293:Sharpr-MPRA regulatory region 6303 [Gene]
  • LOC123038165:Sharpr-MPRA regulatory region 831 [Gene]
  • LOC123038166:Sharpr-MPRA regulatory region 8988 [Gene]
  • LOC123038163:Sharpr-MPRA regulatory region 9008 [Gene]
  • LOC121009684:Sharpr-MPRA regulatory region 9344 [Gene]
  • LOC111828514:Sharpr-MPRA regulatory regions 1012 and 11425 [Gene]
  • WDR5B:WD repeat domain 5B [Gene - HGNC]
  • WDR5B-DT:WDR5B divergent transcript [Gene - HGNC]
  • ZXDC:ZXD family zinc finger C [Gene - OMIM - HGNC]
  • ADCY5:adenylate cyclase 5 [Gene - OMIM - HGNC]
  • ALDH1L1:aldehyde dehydrogenase 1 family member L1 [Gene - OMIM - HGNC]
  • CASR:calcium sensing receptor [Gene - OMIM - HGNC]
  • CHST13:carbohydrate sulfotransferase 13 [Gene - OMIM - HGNC]
  • C3orf22:chromosome 3 open reading frame 22 [Gene - HGNC]
  • CFAP100:cilia and flagella associated protein 100 [Gene - HGNC]
  • CCDC14:coiled-coil domain containing 14 [Gene - OMIM - HGNC]
  • CHCHD6:coiled-coil-helix-coiled-coil-helix domain containing 6 [Gene - OMIM - HGNC]
  • CSTA:cystatin A [Gene - OMIM - HGNC]
  • DTX3L:deltex E3 ubiquitin ligase 3L [Gene - OMIM - HGNC]
  • FAM162A:family with sequence similarity 162 member A [Gene - OMIM - HGNC]
  • HEG1:heart development protein with EGF like domains 1 [Gene - OMIM - HGNC]
  • ILDR1:immunoglobulin like domain containing receptor 1 [Gene - OMIM - HGNC]
  • ITGB5:integrin subunit beta 5 [Gene - OMIM - HGNC]
  • KALRN:kalirin RhoGEF kinase [Gene - OMIM - HGNC]
  • KPNA1:karyopherin subunit alpha 1 [Gene - OMIM - HGNC]
  • LINC02035:long intergenic non-protein coding RNA 2035 [Gene - HGNC]
  • LINC02614:long intergenic non-protein coding RNA 2614 [Gene - HGNC]
  • MIR5002:microRNA 5002 [Gene - HGNC]
  • MIR5092:microRNA 5092 [Gene - HGNC]
  • MIR544B:microRNA 544b [Gene - HGNC]
  • MIR548I1:microRNA 548i-1 [Gene - HGNC]
  • MIR6083:microRNA 6083 [Gene - HGNC]
  • MIR7110:microRNA 7110 [Gene - HGNC]
  • MIX23:mitochondrial matrix import factor 23 [Gene - OMIM - HGNC]
  • MUC13:mucin 13, cell surface associated [Gene - OMIM - HGNC]
  • MYLK:myosin light chain kinase [Gene - OMIM - HGNC]
  • OSBPL11:oxysterol binding protein like 11 [Gene - OMIM - HGNC]
  • PARP14:poly(ADP-ribose) polymerase family member 14 [Gene - OMIM - HGNC]
  • PARP15:poly(ADP-ribose) polymerase family member 15 [Gene - OMIM - HGNC]
  • PARP9:poly(ADP-ribose) polymerase family member 9 [Gene - OMIM - HGNC]
  • PDIA5:protein disulfide isomerase family A member 5 [Gene - OMIM - HGNC]
  • ROPN1:rhophilin associated tail protein 1 [Gene - OMIM - HGNC]
  • ROPN1B:rhophilin associated tail protein 1B [Gene - HGNC]
  • SEMA5B:semaphorin 5B [Gene - OMIM - HGNC]
  • SLC12A8:solute carrier family 12 member 8 [Gene - OMIM - HGNC]
  • SLC15A2:solute carrier family 15 member 2 [Gene - OMIM - HGNC]
  • SLC41A3:solute carrier family 41 member 3 [Gene - OMIM - HGNC]
  • SLC49A4:solute carrier family 49 member 4 [Gene - OMIM - HGNC]
  • SNX4:sorting nexin 4 [Gene - OMIM - HGNC]
  • TXNRD3NB:thioredoxin reductase 3 neighbor [Gene - HGNC]
  • TXNRD3:thioredoxin reductase 3 [Gene - OMIM - HGNC]
  • LOC105374312:uncharacterized LOC105374312 [Gene]
  • UMPS:uridine monophosphate synthetase [Gene - OMIM - HGNC]
  • UROC1:urocanate hydratase 1 [Gene - OMIM - HGNC]
  • ZNF148:zinc finger protein 148 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
3q13.33-21.3
Genomic location:
Preferred name:
GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1
HGVS:
  • NC_000003.12:g.(?_121925147)_(126782249_?)del
  • NC_000003.10:g.(?_123126684)_(127983782_?)del
  • NC_000003.11:g.(?_121643994)_(126501092_?)del
Links:
dbVar: nssv1610314; dbVar: nsv932123
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
SCV000181608ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Dec 17, 2012) 		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

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, SCV000181608.4

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

Last Updated: Feb 20, 2024