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GRCh38/hg38 3q23-24(chr3:141751960-148246189)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:
RCV000051575.6

Allele description [Variation Report for GRCh38/hg38 3q23-24(chr3:141751960-148246189)x1]

GRCh38/hg38 3q23-24(chr3:141751960-148246189)x1

Genes:
  • XRN1:5'-3' exoribonuclease 1 [Gene - OMIM - HGNC]
  • LOC129937690:ATAC-STARR-seq lymphoblastoid active region 20637 [Gene]
  • LOC129937691:ATAC-STARR-seq lymphoblastoid active region 20638 [Gene]
  • LOC129937696:ATAC-STARR-seq lymphoblastoid active region 20640 [Gene]
  • LOC129937701:ATAC-STARR-seq lymphoblastoid active region 20641 [Gene]
  • LOC129937702:ATAC-STARR-seq lymphoblastoid active region 20642 [Gene]
  • LOC129937703:ATAC-STARR-seq lymphoblastoid active region 20643 [Gene]
  • LOC129937704:ATAC-STARR-seq lymphoblastoid active region 20644 [Gene]
  • LOC129937705:ATAC-STARR-seq lymphoblastoid active region 20645 [Gene]
  • LOC129937708:ATAC-STARR-seq lymphoblastoid active region 20647 [Gene]
  • LOC129937709:ATAC-STARR-seq lymphoblastoid active region 20650 [Gene]
  • LOC129937712:ATAC-STARR-seq lymphoblastoid active region 20651 [Gene]
  • LOC129937713:ATAC-STARR-seq lymphoblastoid active region 20652 [Gene]
  • LOC129937714:ATAC-STARR-seq lymphoblastoid active region 20653 [Gene]
  • LOC129937715:ATAC-STARR-seq lymphoblastoid active region 20654 [Gene]
  • LOC129937716:ATAC-STARR-seq lymphoblastoid active region 20655 [Gene]
  • LOC129937717:ATAC-STARR-seq lymphoblastoid active region 20656 [Gene]
  • LOC129937718:ATAC-STARR-seq lymphoblastoid active region 20657 [Gene]
  • LOC129937719:ATAC-STARR-seq lymphoblastoid active region 20658 [Gene]
  • LOC129937720:ATAC-STARR-seq lymphoblastoid active region 20659 [Gene]
  • LOC129937721:ATAC-STARR-seq lymphoblastoid active region 20660 [Gene]
  • LOC129937723:ATAC-STARR-seq lymphoblastoid active region 20663 [Gene]
  • LOC129937724:ATAC-STARR-seq lymphoblastoid active region 20664 [Gene]
  • LOC129937725:ATAC-STARR-seq lymphoblastoid active region 20665 [Gene]
  • LOC129937726:ATAC-STARR-seq lymphoblastoid active region 20666 [Gene]
  • LOC129937727:ATAC-STARR-seq lymphoblastoid active region 20667 [Gene]
  • LOC129937728:ATAC-STARR-seq lymphoblastoid active region 20668 [Gene]
  • LOC129937729:ATAC-STARR-seq lymphoblastoid active region 20669 [Gene]
  • LOC129937730:ATAC-STARR-seq lymphoblastoid active region 20670 [Gene]
  • LOC129937731:ATAC-STARR-seq lymphoblastoid active region 20672 [Gene]
  • LOC129937732:ATAC-STARR-seq lymphoblastoid active region 20674 [Gene]
  • LOC129937733:ATAC-STARR-seq lymphoblastoid active region 20675 [Gene]
  • LOC129937692:ATAC-STARR-seq lymphoblastoid silent region 14780 [Gene]
  • LOC129937693:ATAC-STARR-seq lymphoblastoid silent region 14781 [Gene]
  • LOC129937694:ATAC-STARR-seq lymphoblastoid silent region 14782 [Gene]
  • LOC129937695:ATAC-STARR-seq lymphoblastoid silent region 14783 [Gene]
  • LOC129937697:ATAC-STARR-seq lymphoblastoid silent region 14784 [Gene]
  • LOC129937698:ATAC-STARR-seq lymphoblastoid silent region 14787 [Gene]
  • LOC129937699:ATAC-STARR-seq lymphoblastoid silent region 14788 [Gene]
  • LOC129937700:ATAC-STARR-seq lymphoblastoid silent region 14789 [Gene]
  • LOC129937706:ATAC-STARR-seq lymphoblastoid silent region 14790 [Gene]
  • LOC129937707:ATAC-STARR-seq lymphoblastoid silent region 14791 [Gene]
  • LOC129937710:ATAC-STARR-seq lymphoblastoid silent region 14793 [Gene]
  • LOC129937711:ATAC-STARR-seq lymphoblastoid silent region 14794 [Gene]
  • LOC129937722:ATAC-STARR-seq lymphoblastoid silent region 14800 [Gene]
  • LOC129937734:ATAC-STARR-seq lymphoblastoid silent region 14801 [Gene]
  • ATP1B3:ATPase Na+/K+ transporting subunit beta 3 [Gene - OMIM - HGNC]
  • ATR:ATR serine/threonine kinase [Gene - OMIM - HGNC]
  • LOC126806830:BRD4-independent group 4 enhancer GRCh37_chr3:142203676-142204875 [Gene]
  • LOC126806835:BRD4-independent group 4 enhancer GRCh37_chr3:145274533-145275732 [Gene]
  • LOC126806836:BRD4-independent group 4 enhancer GRCh37_chr3:146105286-146106485 [Gene]
  • LOC115995524:CRISPRi-validated cis-regulatory element chr3.4237 [Gene]
  • LOC115995525:CRISPRi-validated cis-regulatory element chr3.4238 [Gene]
  • LOC115995526:CRISPRi-validated cis-regulatory element chr3.4297 [Gene]
  • GRK7:G protein-coupled receptor kinase 7 [Gene - OMIM - HGNC]
  • LOC126806837:MED14-independent group 3 enhancer GRCh37_chr3:146299468-146300667 [Gene]
  • LOC129389144:MPRA-validated peak4856 silencer [Gene]
  • LOC132088870:Neanderthal introgressed variant-containing enhancer experimental_64869 [Gene]
  • LOC132088873:Neanderthal introgressed variant-containing enhancer experimental_65040 [Gene]
  • LOC132090699:Neanderthal introgressed variant-containing enhancer experimental_65044 [Gene]
  • LOC126806831:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:142677150-142678349 [Gene]
  • LOC126806832:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:143162319-143163518 [Gene]
  • LOC126806833:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:144156282-144157481 [Gene]
  • LOC126806834:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:145071494-145072693 [Gene]
  • PAQR9-AS1:PAQR9 antisense RNA 1 [Gene - HGNC]
  • PLS1-AS1:PLS1 antisense RNA 1 [Gene - HGNC]
  • PLSCR5-AS1:PLSCR5 antisense RNA 1 [Gene - HGNC]
  • SLC9A9-AS1:SLC9A9 antisense RNA 1 [Gene - HGNC]
  • LOC112903842:Sharpr-MPRA regulatory region 12219 [Gene]
  • LOC121048716:Sharpr-MPRA regulatory region 3462 [Gene]
  • LOC123038195:Sharpr-MPRA regulatory region 4576 [Gene]
  • LOC123038194:Sharpr-MPRA regulatory region 4874 [Gene]
  • LOC121048715:Sharpr-MPRA regulatory region 6947 [Gene]
  • LOC112935896:Sharpr-MPRA regulatory region 7236 [Gene]
  • LOC123192011:Sharpr-MPRA regulatory region 7261 [Gene]
  • U2SURP:U2 snRNP associated SURP domain containing [Gene - OMIM - HGNC]
  • LOC110120973:VISTA enhancer hs1043 [Gene]
  • LOC110121014:VISTA enhancer hs1173 [Gene]
  • LOC110121026:VISTA enhancer hs1203 [Gene]
  • LOC110121033:VISTA enhancer hs1224 [Gene]
  • LOC110121146:VISTA enhancer hs1573 [Gene]
  • LOC110121244:VISTA enhancer hs2041 [Gene]
  • LOC110120615:VISTA enhancer hs213 [Gene]
  • LOC110120733:VISTA enhancer hs654 [Gene]
  • ZIC4-AS1:ZIC4 antisense RNA 1 [Gene - HGNC]
  • ZIC1:Zic family member 1 [Gene - OMIM - HGNC]
  • ZIC4:Zic family member 4 [Gene - OMIM - HGNC]
  • CHST2:carbohydrate sulfotransferase 2 [Gene - OMIM - HGNC]
  • DIPK2A:divergent protein kinase domain 2A [Gene - OMIM - HGNC]
  • GK5:glycerol kinase 5 [Gene - OMIM - HGNC]
  • HLMR1:hepatic lncRNA metabolic regulator 1 [Gene - HGNC]
  • LOC124909494:leucine-rich repeat extensin-like protein 5 [Gene]
  • LNCSRLR:lncRNA sorafenib resistance in renal cell carcinoma associated [Gene - HGNC]
  • LINC02010:long intergenic non-protein coding RNA 2010 [Gene - HGNC]
  • LINC02032:long intergenic non-protein coding RNA 2032 [Gene - HGNC]
  • LINC02045:long intergenic non-protein coding RNA 2045 [Gene - HGNC]
  • PLSCR1:phospholipid scramblase 1 [Gene - OMIM - HGNC]
  • PLSCR2:phospholipid scramblase 2 [Gene - OMIM - HGNC]
  • PLSCR4:phospholipid scramblase 4 [Gene - OMIM - HGNC]
  • PLSCR5:phospholipid scramblase family member 5 [Gene - HGNC]
  • PLS1:plastin 1 [Gene - OMIM - HGNC]
  • PCOLCE2:procollagen C-endopeptidase enhancer 2 [Gene - OMIM - HGNC]
  • PLOD2:procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 [Gene - OMIM - HGNC]
  • PAQR9:progestin and adipoQ receptor family member 9 [Gene - OMIM - HGNC]
  • SLC9A9:solute carrier family 9 member A9 [Gene - OMIM - HGNC]
  • TFDP2:transcription factor Dp-2 [Gene - OMIM - HGNC]
  • TRPC1:transient receptor potential cation channel subfamily C member 1 [Gene - OMIM - HGNC]
  • LOC100289361:uncharacterized LOC100289361 [Gene]
  • LOC440982:uncharacterized LOC440982 [Gene]
Variant type:
copy number loss
Cytogenetic location:
3q23-24
Genomic location:
Preferred name:
GRCh38/hg38 3q23-24(chr3:141751960-148246189)x1
HGVS:
  • NC_000003.12:g.(?_141751960)_(148246189_?)del
  • NC_000003.10:g.(?_142953492)_(149446666_?)del
  • NC_000003.11:g.(?_141470802)_(147963976_?)del
Links:
dbVar: nssv577927; dbVar: nsv530098
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
SCV000078923ISCA 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]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not 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, SCV000078923.4

#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