GRCh38/hg38 3q29(chr3:196035777-197658540)x1 AND See cases

Clinical significance:Pathogenic (Last evaluated: Aug 12, 2011)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000053114.4

Allele description [Variation Report for GRCh38/hg38 3q29(chr3:196035777-197658540)x1]

GRCh38/hg38 3q29(chr3:196035777-197658540)x1

Genes:
  • BDH1:3-hydroxybutyrate dehydrogenase 1 [Gene - OMIM - HGNC]
  • LOC115995537:CRISPRi-validated cis-regulatory element chr3.5812 [Gene]
  • LOC115995538:CRISPRi-validated cis-regulatory element chr3.5817 [Gene]
  • DLG1-AS1:DLG1 antisense RNA 1 [Gene - HGNC]
  • FBXO45:F-box protein 45 [Gene - OMIM - HGNC]
  • MELTF-AS1:MELTF antisense RNA 1 [Gene - HGNC]
  • NCBP2AS2:NCBP2 antisense 2 (head to head) [Gene - HGNC]
  • NCBP2-AS1:NCBP2 antisense RNA 1 [Gene - HGNC]
  • SENP5:SUMO specific peptidase 5 [Gene - OMIM - HGNC]
  • LOC112935924:Sharpr-MPRA regulatory region 3422 [Gene]
  • LOC111828515:Sharpr-MPRA regulatory regions 4170 and 8020 [Gene]
  • TM4SF19-AS1:TM4SF19 antisense RNA 1 [Gene - HGNC]
  • TM4SF19-TCTEX1D2:TM4SF19-TCTEX1D2 readthrough (NMD candidate) [Gene - HGNC]
  • TCTEX1D2:Tctex1 domain containing 2 [Gene - OMIM - HGNC]
  • UBXN7:UBX domain protein 7 [Gene - OMIM - HGNC]
  • UBXN7-AS1:UBXN7 antisense RNA 1 [Gene - HGNC]
  • WDR53:WD repeat domain 53 [Gene - OMIM - HGNC]
  • CEP19:centrosomal protein 19 [Gene - OMIM - HGNC]
  • DLG1:discs large MAGUK scaffold protein 1 [Gene - OMIM - HGNC]
  • LINC01063:long intergenic non-protein coding RNA 1063 [Gene - HGNC]
  • LINC02012:long intergenic non-protein coding RNA 2012 [Gene - HGNC]
  • LINC00885:long intergenic non-protein coding RNA 885 [Gene - HGNC]
  • MELTF:melanotransferrin [Gene - OMIM - HGNC]
  • MIR4797:microRNA 4797 [Gene - HGNC]
  • NRROS:negative regulator of reactive oxygen species [Gene - OMIM - HGNC]
  • NCBP2:nuclear cap binding protein subunit 2 [Gene - OMIM - HGNC]
  • PAK2:p21 (RAC1) activated kinase 2 [Gene - OMIM - HGNC]
  • PCYT1A:phosphate cytidylyltransferase 1, choline, alpha [Gene - OMIM - HGNC]
  • PIGX:phosphatidylinositol glycan anchor biosynthesis class X [Gene - OMIM - HGNC]
  • PIGZ:phosphatidylinositol glycan anchor biosynthesis class Z [Gene - OMIM - HGNC]
  • RNF168:ring finger protein 168 [Gene - OMIM - HGNC]
  • SMCO1:single-pass membrane protein with coiled-coil domains 1 [Gene - HGNC]
  • SLC51A:solute carrier family 51 subunit alpha [Gene - OMIM - HGNC]
  • TFRC:transferrin receptor [Gene - OMIM - HGNC]
  • TM4SF19:transmembrane 4 L six family member 19 [Gene - HGNC]
  • ZDHHC19:zinc finger DHHC-type palmitoyltransferase 19 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
3q29
Genomic location:
Preferred name:
GRCh38/hg38 3q29(chr3:196035777-197658540)x1
HGVS:
  • NC_000003.12:g.(?_196035777)_(197658540_?)del
  • NC_000003.10:g.(?_197247045)_(198869808_?)del
  • NC_000003.11:g.(?_195762648)_(197385411_?)del
Links:
dbVar: nssv580099; dbVar: nsv531803
Observations:
1

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000080469ISCA site 6

See additional submitters

criteria provided, single submitter
Pathogenic
(Aug 12, 2011)
not providedclinical testing

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

Description

Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations. Clinical assertions have been curated as described in Kaminsky et al. 2011.

SCV000080469

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 6, SCV000080469.4

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

Last Updated: Dec 17, 2019

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