U.S. flag

An official website of the United States government

GRCh38/hg38 21q22.3(chr21:45138321-46670405)x1 AND See cases

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Aug 12, 2011
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000052864.6

Allele description [Variation Report for GRCh38/hg38 21q22.3(chr21:45138321-46670405)x1]

GRCh38/hg38 21q22.3(chr21:45138321-46670405)x1

Genes:
  • LOC130066851:ATAC-STARR-seq lymphoblastoid active region 18590 [Gene]
  • LOC130066852:ATAC-STARR-seq lymphoblastoid active region 18591 [Gene]
  • LOC130066860:ATAC-STARR-seq lymphoblastoid active region 18594 [Gene]
  • LOC130066861:ATAC-STARR-seq lymphoblastoid active region 18595 [Gene]
  • LOC130066865:ATAC-STARR-seq lymphoblastoid active region 18596 [Gene]
  • LOC130066866:ATAC-STARR-seq lymphoblastoid active region 18597 [Gene]
  • LOC130066867:ATAC-STARR-seq lymphoblastoid active region 18598 [Gene]
  • LOC130066871:ATAC-STARR-seq lymphoblastoid active region 18599 [Gene]
  • LOC130066874:ATAC-STARR-seq lymphoblastoid active region 18600 [Gene]
  • LOC130066877:ATAC-STARR-seq lymphoblastoid active region 18601 [Gene]
  • LOC130066878:ATAC-STARR-seq lymphoblastoid active region 18602 [Gene]
  • LOC130066879:ATAC-STARR-seq lymphoblastoid active region 18603 [Gene]
  • LOC130066880:ATAC-STARR-seq lymphoblastoid active region 18604 [Gene]
  • LOC130066883:ATAC-STARR-seq lymphoblastoid active region 18605 [Gene]
  • LOC130066884:ATAC-STARR-seq lymphoblastoid active region 18606 [Gene]
  • LOC130066887:ATAC-STARR-seq lymphoblastoid active region 18607 [Gene]
  • LOC130066850:ATAC-STARR-seq lymphoblastoid silent region 13401 [Gene]
  • LOC130066853:ATAC-STARR-seq lymphoblastoid silent region 13402 [Gene]
  • LOC130066854:ATAC-STARR-seq lymphoblastoid silent region 13403 [Gene]
  • LOC130066855:ATAC-STARR-seq lymphoblastoid silent region 13405 [Gene]
  • LOC130066856:ATAC-STARR-seq lymphoblastoid silent region 13406 [Gene]
  • LOC130066857:ATAC-STARR-seq lymphoblastoid silent region 13407 [Gene]
  • LOC130066858:ATAC-STARR-seq lymphoblastoid silent region 13408 [Gene]
  • LOC130066859:ATAC-STARR-seq lymphoblastoid silent region 13409 [Gene]
  • LOC130066862:ATAC-STARR-seq lymphoblastoid silent region 13410 [Gene]
  • LOC130066863:ATAC-STARR-seq lymphoblastoid silent region 13411 [Gene]
  • LOC130066864:ATAC-STARR-seq lymphoblastoid silent region 13412 [Gene]
  • LOC130066868:ATAC-STARR-seq lymphoblastoid silent region 13413 [Gene]
  • LOC130066869:ATAC-STARR-seq lymphoblastoid silent region 13414 [Gene]
  • LOC130066870:ATAC-STARR-seq lymphoblastoid silent region 13416 [Gene]
  • LOC130066872:ATAC-STARR-seq lymphoblastoid silent region 13417 [Gene]
  • LOC130066873:ATAC-STARR-seq lymphoblastoid silent region 13418 [Gene]
  • LOC130066875:ATAC-STARR-seq lymphoblastoid silent region 13419 [Gene]
  • LOC130066876:ATAC-STARR-seq lymphoblastoid silent region 13420 [Gene]
  • LOC130066881:ATAC-STARR-seq lymphoblastoid silent region 13421 [Gene]
  • LOC130066882:ATAC-STARR-seq lymphoblastoid silent region 13422 [Gene]
  • LOC130066885:ATAC-STARR-seq lymphoblastoid silent region 13424 [Gene]
  • LOC130066886:ATAC-STARR-seq lymphoblastoid silent region 13425 [Gene]
  • LOC126653402:BRD4-independent group 4 enhancer GRCh37_chr21:46785000-46786199 [Gene]
  • LOC126653404:BRD4-independent group 4 enhancer GRCh37_chr21:47278335-47279534 [Gene]
  • COL18A1-AS1:COL18A1 antisense RNA 1 [Gene - HGNC]
  • COL18A1-AS2:COL18A1 antisense RNA 2 [Gene - HGNC]
  • COL6A2-DT:COL6A2 divergent transcript [Gene - HGNC]
  • LOC116309125:CRISPRi-validated cis-regulatory element chr21.1536 [Gene]
  • DIP2A-IT1:DIP2A intronic transcript 1 [Gene - HGNC]
  • FTCD-AS1:FTCD antisense RNA 1 [Gene - HGNC]
  • MCM3AP-AS1:MCM3AP antisense RNA 1 [Gene - HGNC]
  • LOC126653401:MED14-independent group 3 enhancer GRCh37_chr21:46699476-46700675 [Gene]
  • LOC126653403:MED14-independent group 3 enhancer GRCh37_chr21:47053121-47054320 [Gene]
  • LOC129391251:MPRA-validated peak4424 silencer [Gene]
  • LOC129391252:MPRA-validated peak4426 silencer [Gene]
  • LOC129391253:MPRA-validated peak4427 silencer [Gene]
  • LOC129391254:MPRA-validated peak4431 silencer [Gene]
  • LOC112694752:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:46783494-46784693 [Gene]
  • PCBP3-AS1:PCBP3 antisense RNA 1 [Gene - HGNC]
  • S100B:S100 calcium binding protein B [Gene - OMIM - HGNC]
  • LOC121853033:Sharpr-MPRA regulatory region 12001 [Gene]
  • LOC112694754:Sharpr-MPRA regulatory region 1466 [Gene]
  • LOC121627927:Sharpr-MPRA regulatory region 1559 [Gene]
  • LOC125418088:Sharpr-MPRA regulatory region 3768 [Gene]
  • LOC112694753:Sharpr-MPRA regulatory region 3947 [Gene]
  • LOC121853034:Sharpr-MPRA regulatory region 4411 [Gene]
  • LOC121627926:Sharpr-MPRA regulatory region 4412 [Gene]
  • LOC125418086:Sharpr-MPRA regulatory region 7423 [Gene]
  • LOC125418087:Sharpr-MPRA regulatory region 9072 [Gene]
  • ADARB1:adenosine deaminase RNA specific B1 [Gene - OMIM - HGNC]
  • BNAT1:breast cancer associated ESR1 regulating natural antisense transcript 1 [Gene - HGNC]
  • C21orf58:chromosome 21 open reading frame 58 [Gene - HGNC]
  • COL6A1:collagen type VI alpha 1 chain [Gene - OMIM - HGNC]
  • COL6A2:collagen type VI alpha 2 chain [Gene - OMIM - HGNC]
  • COL18A1:collagen type XVIII alpha 1 chain [Gene - OMIM - HGNC]
  • DIP2A:disco interacting protein 2 homolog A [Gene - OMIM - HGNC]
  • FTCD:formimidoyltransferase cyclodeaminase [Gene - OMIM - HGNC]
  • LSS:lanosterol synthase [Gene - OMIM - HGNC]
  • LINC01694:long intergenic non-protein coding RNA 1694 [Gene - HGNC]
  • LINC00205:long intergenic non-protein coding RNA 205 [Gene - HGNC]
  • LINC00315:long intergenic non-protein coding RNA 315 [Gene - HGNC]
  • LINC00316:long intergenic non-protein coding RNA 316 [Gene - HGNC]
  • LINC00334:long intergenic non-protein coding RNA 334 [Gene - HGNC]
  • MIR6815:microRNA 6815 [Gene - HGNC]
  • MCM3AP:minichromosome maintenance complex component 3 associated protein [Gene - OMIM - HGNC]
  • PCNT:pericentrin [Gene - OMIM - HGNC]
  • PCBP3:poly(rC) binding protein 3 [Gene - OMIM - HGNC]
  • POFUT2:protein O-fucosyltransferase 2 [Gene - OMIM - HGNC]
  • PRMT2:protein arginine methyltransferase 2 [Gene - OMIM - HGNC]
  • SNORD159:small nucleolar RNA, C/D box 159 [Gene - HGNC]
  • SLC19A1:solute carrier family 19 member 1 [Gene - OMIM - HGNC]
  • SPATC1L:spermatogenesis and centriole associated 1 like [Gene - OMIM - HGNC]
  • LOC101928796:uncharacterized LOC101928796 [Gene]
  • LOC128092249:uncharacterized LOC128092249 [Gene]
  • YBEY:ybeY metalloendoribonuclease [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
GRCh38/hg38 21q22.3(chr21:45138321-46670405)x1
HGVS:
  • NC_000021.9:g.(?_45138321)_(46670405_?)del
  • NC_000021.7:g.(?_45382664)_(46914745_?)del
  • NC_000021.8:g.(?_46558236)_(48090317_?)del
Links:
dbVar: nssv577835; dbVar: nssv577837; dbVar: nsv531579
Observations:
2

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000190898ISCA site 17

See additional submitters

criteria provided, single submitter

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

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

SCV000190899ISCA site 4

See additional submitters

criteria provided, single submitter

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

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes2not 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 17, SCV000190898.2

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

From ISCA site 4, SCV000190899.3

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

Last Updated: May 7, 2024