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GRCh38/hg38 5q21.1-22.2(chr5:102373396-113594030)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:
RCV000053523.6

Allele description [Variation Report for GRCh38/hg38 5q21.1-22.2(chr5:102373396-113594030)x1]

GRCh38/hg38 5q21.1-22.2(chr5:102373396-113594030)x1

Genes:
  • APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
  • LOC129994297:ATAC-STARR-seq lymphoblastoid active region 22854 [Gene]
  • LOC129994300:ATAC-STARR-seq lymphoblastoid active region 22856 [Gene]
  • LOC129994302:ATAC-STARR-seq lymphoblastoid active region 22858 [Gene]
  • LOC129994303:ATAC-STARR-seq lymphoblastoid active region 22859 [Gene]
  • LOC129994304:ATAC-STARR-seq lymphoblastoid active region 22860 [Gene]
  • LOC129994307:ATAC-STARR-seq lymphoblastoid active region 22861 [Gene]
  • LOC129994308:ATAC-STARR-seq lymphoblastoid active region 22862 [Gene]
  • LOC129994309:ATAC-STARR-seq lymphoblastoid active region 22863 [Gene]
  • LOC129994310:ATAC-STARR-seq lymphoblastoid active region 22864 [Gene]
  • LOC129994312:ATAC-STARR-seq lymphoblastoid active region 22867 [Gene]
  • LOC129994313:ATAC-STARR-seq lymphoblastoid active region 22868 [Gene]
  • LOC129994315:ATAC-STARR-seq lymphoblastoid active region 22869 [Gene]
  • LOC129994317:ATAC-STARR-seq lymphoblastoid active region 22870 [Gene]
  • LOC129994321:ATAC-STARR-seq lymphoblastoid active region 22872 [Gene]
  • LOC129994322:ATAC-STARR-seq lymphoblastoid active region 22873 [Gene]
  • LOC129994323:ATAC-STARR-seq lymphoblastoid active region 22874 [Gene]
  • LOC129994324:ATAC-STARR-seq lymphoblastoid active region 22875 [Gene]
  • LOC129994328:ATAC-STARR-seq lymphoblastoid active region 22876 [Gene]
  • LOC129994332:ATAC-STARR-seq lymphoblastoid active region 22878 [Gene]
  • LOC129994333:ATAC-STARR-seq lymphoblastoid active region 22879 [Gene]
  • LOC129994334:ATAC-STARR-seq lymphoblastoid active region 22880 [Gene]
  • LOC129994336:ATAC-STARR-seq lymphoblastoid active region 22881 [Gene]
  • LOC129994337:ATAC-STARR-seq lymphoblastoid active region 22882 [Gene]
  • LOC129994342:ATAC-STARR-seq lymphoblastoid active region 22884 [Gene]
  • LOC129994343:ATAC-STARR-seq lymphoblastoid active region 22885 [Gene]
  • LOC129994344:ATAC-STARR-seq lymphoblastoid active region 22886 [Gene]
  • LOC129994345:ATAC-STARR-seq lymphoblastoid active region 22887 [Gene]
  • LOC129994346:ATAC-STARR-seq lymphoblastoid active region 22888 [Gene]
  • LOC129994347:ATAC-STARR-seq lymphoblastoid active region 22889 [Gene]
  • LOC129994348:ATAC-STARR-seq lymphoblastoid active region 22890 [Gene]
  • LOC129994350:ATAC-STARR-seq lymphoblastoid active region 22891 [Gene]
  • LOC129994354:ATAC-STARR-seq lymphoblastoid active region 22892 [Gene]
  • LOC129994355:ATAC-STARR-seq lymphoblastoid active region 22893 [Gene]
  • LOC129994356:ATAC-STARR-seq lymphoblastoid active region 22894 [Gene]
  • LOC129994357:ATAC-STARR-seq lymphoblastoid active region 22895 [Gene]
  • LOC129994358:ATAC-STARR-seq lymphoblastoid active region 22896 [Gene]
  • LOC129994359:ATAC-STARR-seq lymphoblastoid active region 22897 [Gene]
  • LOC129994360:ATAC-STARR-seq lymphoblastoid active region 22898 [Gene]
  • LOC129994361:ATAC-STARR-seq lymphoblastoid active region 22899 [Gene]
  • LOC129994363:ATAC-STARR-seq lymphoblastoid active region 22900 [Gene]
  • LOC129994364:ATAC-STARR-seq lymphoblastoid active region 22901 [Gene]
  • LOC129994365:ATAC-STARR-seq lymphoblastoid active region 22903 [Gene]
  • LOC129994368:ATAC-STARR-seq lymphoblastoid active region 22904 [Gene]
  • LOC129994371:ATAC-STARR-seq lymphoblastoid active region 22910 [Gene]
  • LOC129994375:ATAC-STARR-seq lymphoblastoid active region 22913 [Gene]
  • LOC129994377:ATAC-STARR-seq lymphoblastoid active region 22914 [Gene]
  • LOC129994378:ATAC-STARR-seq lymphoblastoid active region 22915 [Gene]
  • LOC129994379:ATAC-STARR-seq lymphoblastoid active region 22916 [Gene]
  • LOC129994381:ATAC-STARR-seq lymphoblastoid active region 22921 [Gene]
  • LOC129994298:ATAC-STARR-seq lymphoblastoid silent region 16207 [Gene]
  • LOC129994299:ATAC-STARR-seq lymphoblastoid silent region 16208 [Gene]
  • LOC129994301:ATAC-STARR-seq lymphoblastoid silent region 16209 [Gene]
  • LOC129994305:ATAC-STARR-seq lymphoblastoid silent region 16210 [Gene]
  • LOC129994306:ATAC-STARR-seq lymphoblastoid silent region 16211 [Gene]
  • LOC129994311:ATAC-STARR-seq lymphoblastoid silent region 16212 [Gene]
  • LOC129994314:ATAC-STARR-seq lymphoblastoid silent region 16213 [Gene]
  • LOC129994316:ATAC-STARR-seq lymphoblastoid silent region 16214 [Gene]
  • LOC129994318:ATAC-STARR-seq lymphoblastoid silent region 16215 [Gene]
  • LOC129994319:ATAC-STARR-seq lymphoblastoid silent region 16216 [Gene]
  • LOC129994320:ATAC-STARR-seq lymphoblastoid silent region 16217 [Gene]
  • LOC129994325:ATAC-STARR-seq lymphoblastoid silent region 16218 [Gene]
  • LOC129994326:ATAC-STARR-seq lymphoblastoid silent region 16219 [Gene]
  • LOC129994327:ATAC-STARR-seq lymphoblastoid silent region 16220 [Gene]
  • LOC129994329:ATAC-STARR-seq lymphoblastoid silent region 16221 [Gene]
  • LOC129994330:ATAC-STARR-seq lymphoblastoid silent region 16222 [Gene]
  • LOC129994331:ATAC-STARR-seq lymphoblastoid silent region 16223 [Gene]
  • LOC129994335:ATAC-STARR-seq lymphoblastoid silent region 16224 [Gene]
  • LOC129994338:ATAC-STARR-seq lymphoblastoid silent region 16225 [Gene]
  • LOC129994339:ATAC-STARR-seq lymphoblastoid silent region 16226 [Gene]
  • LOC129994340:ATAC-STARR-seq lymphoblastoid silent region 16227 [Gene]
  • LOC129994341:ATAC-STARR-seq lymphoblastoid silent region 16228 [Gene]
  • LOC129994349:ATAC-STARR-seq lymphoblastoid silent region 16229 [Gene]
  • LOC129994351:ATAC-STARR-seq lymphoblastoid silent region 16230 [Gene]
  • LOC129994352:ATAC-STARR-seq lymphoblastoid silent region 16231 [Gene]
  • LOC129994353:ATAC-STARR-seq lymphoblastoid silent region 16232 [Gene]
  • LOC129994362:ATAC-STARR-seq lymphoblastoid silent region 16233 [Gene]
  • LOC129994366:ATAC-STARR-seq lymphoblastoid silent region 16234 [Gene]
  • LOC129994367:ATAC-STARR-seq lymphoblastoid silent region 16235 [Gene]
  • LOC129994369:ATAC-STARR-seq lymphoblastoid silent region 16236 [Gene]
  • LOC129994370:ATAC-STARR-seq lymphoblastoid silent region 16237 [Gene]
  • LOC129994372:ATAC-STARR-seq lymphoblastoid silent region 16238 [Gene]
  • LOC129994373:ATAC-STARR-seq lymphoblastoid silent region 16239 [Gene]
  • LOC129994374:ATAC-STARR-seq lymphoblastoid silent region 16240 [Gene]
  • LOC129994376:ATAC-STARR-seq lymphoblastoid silent region 16241 [Gene]
  • LOC129994380:ATAC-STARR-seq lymphoblastoid silent region 16242 [Gene]
  • LOC129994382:ATAC-STARR-seq lymphoblastoid silent region 16243 [Gene]
  • LOC126807470:BRD4-independent group 4 enhancer GRCh37_chr5:103707754-103708953 [Gene]
  • LOC126807475:BRD4-independent group 4 enhancer GRCh37_chr5:111333199-111334398 [Gene]
  • LOC126807476:BRD4-independent group 4 enhancer GRCh37_chr5:111496090-111497289 [Gene]
  • LOC126807468:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:102363594-102364793 [Gene]
  • LOC126807471:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:106620899-106622098 [Gene]
  • LOC126807473:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:107060476-107061675 [Gene]
  • LOC126807478:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:112417522-112418721 [Gene]
  • EPB41L4A-AS1:EPB41L4A antisense RNA 1 [Gene - HGNC]
  • EPB41L4A-DT:EPB41L4A divergent transcript [Gene - HGNC]
  • FBXL17:F-box and leucine rich repeat protein 17 [Gene - OMIM - HGNC]
  • FER:FER tyrosine kinase [Gene - OMIM - HGNC]
  • MAN2A1-DT:MAN2A1 divergent transcript [Gene - HGNC]
  • MCC:MCC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
  • LOC126807469:MED14-independent group 3 enhancer GRCh37_chr5:103652082-103653281 [Gene]
  • LOC126807472:MED14-independent group 3 enhancer GRCh37_chr5:106946073-106947272 [Gene]
  • LOC126807474:MED14-independent group 3 enhancer GRCh37_chr5:110865742-110866941 [Gene]
  • LOC129389333:MPRA-validated peak5381 silencer [Gene]
  • LOC129389334:MPRA-validated peak5386 silencer [Gene]
  • LOC129389335:MPRA-validated peak5387 silencer [Gene]
  • LOC129389336:MPRA-validated peak5393 silencer [Gene]
  • LOC129389337:MPRA-validated peak5394 silencer [Gene]
  • LOC129389338:MPRA-validated peak5404 silencer [Gene]
  • LOC129389339:MPRA-validated peak5405 silencer [Gene]
  • LOC129389340:MPRA-validated peak5407 silencer [Gene]
  • LOC129389341:MPRA-validated peak5410 silencer [Gene]
  • LOC129389342:MPRA-validated peak5411 silencer [Gene]
  • LOC129389343:MPRA-validated peak5412 silencer [Gene]
  • LOC129389344:MPRA-validated peak5419 silencer [Gene]
  • LOC129389345:MPRA-validated peak5421 silencer [Gene]
  • LOC129389346:MPRA-validated peak5422 silencer [Gene]
  • LOC129389347:MPRA-validated peak5423 silencer [Gene]
  • NREP-AS1:NREP antisense RNA 1 [Gene - HGNC]
  • LOC132089159:Neanderthal introgressed variant-containing enhancer experimental_80648 [Gene]
  • LOC132089160:Neanderthal introgressed variant-containing enhancer experimental_80715 [Gene]
  • LOC126807477:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:112226954-112228153 [Gene]
  • LOC126807479:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:112502443-112503642 [Gene]
  • STARD4-AS1:STARD4 antisense RNA 1 [Gene - HGNC]
  • LOC121725214:Sharpr-MPRA regulatory region 12983 [Gene]
  • LOC123497950:Sharpr-MPRA regulatory region 13215 [Gene]
  • LOC121079954:Sharpr-MPRA regulatory region 13332 [Gene]
  • LOC121079957:Sharpr-MPRA regulatory region 13961 [Gene]
  • LOC121079952:Sharpr-MPRA regulatory region 14586 [Gene]
  • LOC121079956:Sharpr-MPRA regulatory region 14787 [Gene]
  • LOC121725213:Sharpr-MPRA regulatory region 1653 [Gene]
  • LOC121079953:Sharpr-MPRA regulatory region 1662 [Gene]
  • LOC123497951:Sharpr-MPRA regulatory region 1675 [Gene]
  • LOC112997552:Sharpr-MPRA regulatory region 2532 [Gene]
  • LOC121079955:Sharpr-MPRA regulatory region 5089 [Gene]
  • LOC123497947:Sharpr-MPRA regulatory region 5849 [Gene]
  • LOC123497953:Sharpr-MPRA regulatory region 6283 [Gene]
  • LOC123497949:Sharpr-MPRA regulatory region 6746 [Gene]
  • LOC121725212:Sharpr-MPRA regulatory region 6875 [Gene]
  • LOC123497946:Sharpr-MPRA regulatory region 7406 [Gene]
  • LOC123497954:Sharpr-MPRA regulatory region 7502 [Gene]
  • LOC123497948:Sharpr-MPRA regulatory region 7585 [Gene]
  • LOC121725211:Sharpr-MPRA regulatory region 8638 [Gene]
  • LOC112997553:Sharpr-MPRA regulatory region 9882 [Gene]
  • STARD4:StAR related lipid transfer domain containing 4 [Gene - OMIM - HGNC]
  • LOC110121070:VISTA enhancer hs1345 [Gene]
  • LOC110121176:VISTA enhancer hs1649 [Gene]
  • LOC110121194:VISTA enhancer hs1734 [Gene]
  • WDR36:WD repeat domain 36 [Gene - OMIM - HGNC]
  • YTHDC2:YTH N6-methyladenosine RNA binding protein C2 [Gene - OMIM - HGNC]
  • CAMK4:calcium/calmodulin dependent protein kinase IV [Gene - OMIM - HGNC]
  • DCP2:decapping mRNA 2 [Gene - OMIM - HGNC]
  • PPIP5K2:diphosphoinositol pentakisphosphate kinase 2 [Gene - OMIM - HGNC]
  • EFNA5:ephrin A5 [Gene - OMIM - HGNC]
  • EPB41L4A:erythrocyte membrane protein band 4.1 like 4A [Gene - OMIM - HGNC]
  • GIN1:gypsy retrotransposon integrase 1 [Gene - HGNC]
  • LINC01023:long intergenic non-protein coding RNA 1023 [Gene - HGNC]
  • LINC01848:long intergenic non-protein coding RNA 1848 [Gene - HGNC]
  • LINC01950:long intergenic non-protein coding RNA 1950 [Gene - HGNC]
  • LINC02115:long intergenic non-protein coding RNA 2115 [Gene - HGNC]
  • LINC02200:long intergenic non-protein coding RNA 2200 [Gene - HGNC]
  • LINC00491:long intergenic non-protein coding RNA 491 [Gene - HGNC]
  • LINC00492:long intergenic non-protein coding RNA 492 [Gene - HGNC]
  • MACIR:macrophage immunometabolism regulator [Gene - OMIM - HGNC]
  • MAN2A1:mannosidase alpha class 2A member 1 [Gene - OMIM - HGNC]
  • MIR548F3:microRNA 548f-3 [Gene - HGNC]
  • NREP:neuronal regeneration related protein [Gene - OMIM - HGNC]
  • NUDT12:nudix hydrolase 12 [Gene - OMIM - HGNC]
  • PAM:peptidylglycine alpha-amidating monooxygenase [Gene - OMIM - HGNC]
  • PJA2:praja ring finger ubiquitin ligase 2 [Gene - OMIM - HGNC]
  • REEP5:receptor accessory protein 5 [Gene - OMIM - HGNC]
  • SRP19:signal recognition particle 19 [Gene - OMIM - HGNC]
  • SNORA13:small nucleolar RNA, H/ACA box 13 [Gene - HGNC]
  • SLC25A46:solute carrier family 25 member 46 [Gene - OMIM - HGNC]
  • SLCO6A1:solute carrier organic anion transporter family member 6A1 [Gene - OMIM - HGNC]
  • TSSK1B:testis specific serine kinase 1B [Gene - OMIM - HGNC]
  • TSLP:thymic stromal lymphopoietin [Gene - OMIM - HGNC]
  • TMEM232:transmembrane protein 232 [Gene - OMIM - HGNC]
  • LOC101927023:uncharacterized LOC101927023 [Gene]
  • LOC102467216:uncharacterized LOC102467216 [Gene]
  • LOC105379109:uncharacterized LOC105379109 [Gene]
  • LOC285638:uncharacterized LOC285638 [Gene]
Variant type:
copy number loss
Cytogenetic location:
5q21.1-22.2
Genomic location:
Preferred name:
GRCh38/hg38 5q21.1-22.2(chr5:102373396-113594030)x1
HGVS:
  • NC_000005.10:g.(?_102373396)_(113594030_?)del
  • NC_000005.8:g.(?_101736999)_(112957626_?)del
  • NC_000005.9:g.(?_101709100)_(112929727_?)del
Links:
dbVar: nssv578071; dbVar: nsv532197
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
SCV000080881ISCA site 15

See additional submitters

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not 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 ISCA site 15, SCV000080881.4

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

Last Updated: May 7, 2024