GRCh38/hg38 12q13.3-14.1(chr12:57041158-60273934)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:
RCV000052814.4

Allele description [Variation Report for GRCh38/hg38 12q13.3-14.1(chr12:57041158-60273934)x1]

GRCh38/hg38 12q13.3-14.1(chr12:57041158-60273934)x1

Genes:
  • AGAP2-AS1:AGAP2 antisense RNA 1 [Gene - HGNC]
  • ATP23:ATP23 metallopeptidase and ATP synthase assembly factor homolog [Gene - HGNC]
  • AGAP2:ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 [Gene - OMIM - HGNC]
  • CTDSP2:CTD small phosphatase 2 [Gene - OMIM - HGNC]
  • DDIT3:DNA damage inducible transcript 3 [Gene - OMIM - HGNC]
  • EEF1AKMT3:EEF1A lysine methyltransferase 3 [Gene - OMIM - HGNC]
  • GIHCG:GIHCG inhibitor of miR-200b/200a/429 expression [Gene - HGNC]
  • GLI1:GLI family zinc finger 1 [Gene - OMIM - HGNC]
  • LRP1:LDL receptor related protein 1 [Gene - OMIM - HGNC]
  • LRP1-AS:LRP1 antisense RNA [Gene - HGNC]
  • NDUFA4L2:NDUFA4 mitochondrial complex associated like 2 [Gene - HGNC]
  • NAB2:NGFI-A binding protein 2 [Gene - OMIM - HGNC]
  • OS9:OS9 endoplasmic reticulum lectin [Gene - OMIM - HGNC]
  • R3HDM2:R3H domain containing 2 [Gene - HGNC]
  • ARHGAP9:Rho GTPase activating protein 9 [Gene - OMIM - HGNC]
  • ARHGEF25:Rho guanine nucleotide exchange factor 25 [Gene - OMIM - HGNC]
  • STAC3:SH3 and cysteine rich domain 3 [Gene - OMIM - HGNC]
  • LOC112163619:Sharpr-MPRA regulatory region 15392 [Gene]
  • LOC112163617:Sharpr-MPRA regulatory region 225 [Gene]
  • LOC112163618:Sharpr-MPRA regulatory region 358 [Gene]
  • LOC112163615:Sharpr-MPRA regulatory region 4597 [Gene]
  • TSFM:Ts translation elongation factor, mitochondrial [Gene - OMIM - HGNC]
  • LOC110121363:VISTA enhancer hs1427 [Gene]
  • LOC110121374:VISTA enhancer hs1468 [Gene]
  • AVIL:advillin [Gene - OMIM - HGNC]
  • B4GALNT1:beta-1,4-N-acetyl-galactosaminyltransferase 1 [Gene - OMIM - HGNC]
  • CDK4:cyclin dependent kinase 4 [Gene - OMIM - HGNC]
  • CYP27B1:cytochrome P450 family 27 subfamily B member 1 [Gene - OMIM - HGNC]
  • DTX3:deltex E3 ubiquitin ligase 3 [Gene - OMIM - HGNC]
  • DCTN2:dynactin subunit 2 [Gene - OMIM - HGNC]
  • INHBC:inhibin subunit beta C [Gene - OMIM - HGNC]
  • INHBE:inhibin subunit beta E [Gene - OMIM - HGNC]
  • KIF5A:kinesin family member 5A [Gene - OMIM - HGNC]
  • LRIG3:leucine rich repeats and immunoglobulin like domains 3 [Gene - OMIM - HGNC]
  • LINC02388:long intergenic non-protein coding RNA 2388 [Gene - HGNC]
  • LINC02403:long intergenic non-protein coding RNA 2403 [Gene - HGNC]
  • LINC02448:long intergenic non-protein coding RNA 2448 [Gene - HGNC]
  • MARCHF9:membrane associated ring-CH-type finger 9 [Gene - OMIM - HGNC]
  • MARS1:methionyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
  • MBD6:methyl-CpG binding domain protein 6 [Gene - HGNC]
  • METTL1:methyltransferase like 1 [Gene - OMIM - HGNC]
  • MIR1228:microRNA 1228 [Gene - HGNC]
  • MIR26A2:microRNA 26a-2 [Gene - OMIM - HGNC]
  • MIR616:microRNA 616 [Gene - OMIM - HGNC]
  • MIR6758:microRNA 6758 [Gene - HGNC]
  • MIR6759:microRNA 6759 [Gene - HGNC]
  • MYO1A:myosin IA [Gene - OMIM - HGNC]
  • NXPH4:neurexophilin 4 [Gene - OMIM - HGNC]
  • NEMP1:nuclear envelope integral membrane protein 1 [Gene - OMIM - HGNC]
  • PIP4K2C:phosphatidylinositol-5-phosphate 4-kinase type 2 gamma [Gene - OMIM - HGNC]
  • SHMT2:serine hydroxymethyltransferase 2 [Gene - OMIM - HGNC]
  • STAT6:signal transducer and activator of transcription 6 [Gene - OMIM - HGNC]
  • SLC16A7:solute carrier family 16 member 7 [Gene - OMIM - HGNC]
  • SLC26A10:solute carrier family 26 member 10 [Gene - HGNC]
  • TSPAN31:tetraspanin 31 [Gene - OMIM - HGNC]
  • LOC100506869:uncharacterized LOC100506869 [Gene]
  • LOC101927583:uncharacterized LOC101927583 [Gene]
  • LOC283387:uncharacterized LOC283387 [Gene]
Variant type:
copy number loss
Cytogenetic location:
12q13.3-14.1
Genomic location:
Preferred name:
GRCh38/hg38 12q13.3-14.1(chr12:57041158-60273934)x1
HGVS:
  • NC_000012.12:g.(?_57041158)_(60273934_?)del
  • NC_000012.10:g.(?_55721209)_(58953982_?)del
  • NC_000012.11:g.(?_57434942)_(60667715_?)del
Links:
dbVar: nssv577389; dbVar: nsv531531
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
SCV000080168ISCA site 15

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.

SCV000080168

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 15, SCV000080168.4

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

Last Updated: Nov 2, 2019

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