GRCh38/hg38 1p36.32-36.21(chr1:4898439-12911913)x1 AND See cases

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

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000137461.3

Allele description [Variation Report for GRCh38/hg38 1p36.32-36.21(chr1:4898439-12911913)x1]

GRCh38/hg38 1p36.32-36.21(chr1:4898439-12911913)x1

Genes:
  • LOC108281186:AJAP1-NPHP4 intergenic nontranscribed DNase I hypersensitive site-defined enhancer [Gene]
  • C1orf167-AS1:C1orf167 antisense RNA 1 [Gene - HGNC]
  • CAMTA1-AS1:CAMTA1 antisense RNA 1 [Gene - HGNC]
  • CAMTA1-AS2:CAMTA1 antisense RNA 2 [Gene - HGNC]
  • CAMTA1-DT:CAMTA1 divergent transcript [Gene - HGNC]
  • CAMTA1-IT1:CAMTA1 intronic transcript 1 [Gene - HGNC]
  • CENPS-CORT:CENPS-CORT readthrough [Gene - HGNC]
  • DFFA:DNA fragmentation factor subunit alpha [Gene - OMIM - HGNC]
  • DNAJC11:DnaJ heat shock protein family (Hsp40) member C11 [Gene - OMIM - HGNC]
  • ENO1-AS1:ENO1 antisense RNA 1 [Gene - HGNC]
  • ERRFI1:ERBB receptor feedback inhibitor 1 [Gene - OMIM - HGNC]
  • EXOSC10-AS1:EXOSC10 antisense RNA 1 [Gene - HGNC]
  • FBXO2:F-box protein 2 [Gene - OMIM - HGNC]
  • FBXO44:F-box protein 44 [Gene - OMIM - HGNC]
  • FBXO6:F-box protein 6 [Gene - OMIM - HGNC]
  • GPR153:G protein-coupled receptor 153 [Gene - OMIM - HGNC]
  • GPR157:G protein-coupled receptor 157 [Gene - HGNC]
  • KIAA2013:KIAA2013 [Gene - HGNC]
  • MIR34AHG:MIR34A host gene [Gene - HGNC]
  • MTOR-AS1:MTOR antisense RNA 1 [Gene - HGNC]
  • LOC111591499:NFE2L2 motif-containing MPRA enhancer 265 [Gene]
  • NPPA-AS1:NPPA antisense RNA 1 [Gene - HGNC]
  • PHF13:PHD finger protein 13 [Gene - HGNC]
  • PIK3CD-AS1:PIK3CD antisense RNA 1 [Gene - HGNC]
  • PIK3CD-AS2:PIK3CD antisense RNA 2 [Gene - HGNC]
  • PRAMEF10:PRAME family member 10 [Gene - HGNC]
  • PRAMEF11:PRAME family member 11 [Gene - HGNC]
  • PRAMEF12:PRAME family member 12 [Gene - HGNC]
  • PRAMEF1:PRAME family member 1 [Gene - HGNC]
  • PRAMEF2:PRAME family member 2 [Gene - HGNC]
  • PRAMEF4:PRAME family member 4 [Gene - HGNC]
  • PARK7:Parkinsonism associated deglycase [Gene - OMIM - HGNC]
  • RERE-AS1:RERE antisense RNA 1 [Gene - HGNC]
  • RNU5E-1:RNA, U5E small nuclear 1 [Gene - HGNC]
  • LOC108281189:RPL7AP18-LOC102724539 intergenic ENCODE-defined enhancer [Gene]
  • LOC112590813:Sharpr-MPRA regulatory region 11871 [Gene]
  • LOC112590822:Sharpr-MPRA regulatory region 13854 [Gene]
  • LOC112577472:Sharpr-MPRA regulatory region 3946 [Gene]
  • LOC112577487:Sharpr-MPRA regulatory region 4366 [Gene]
  • LOC112577488:Sharpr-MPRA regulatory region 5682 [Gene]
  • LOC112590823:Sharpr-MPRA regulatory region 7894 [Gene]
  • LOC112577486:Sharpr-MPRA regulatory region 8260 [Gene]
  • LOC112590825:Sharpr-MPRA regulatory region 8288 [Gene]
  • LOC112590821:Sharpr-MPRA regulatory region 865 [Gene]
  • TARDBP:TAR DNA binding protein [Gene - OMIM - HGNC]
  • THAP3:THAP domain containing 3 [Gene - OMIM - HGNC]
  • TNFRSF1B:TNF receptor superfamily member 1B [Gene - OMIM - HGNC]
  • TNFRSF25:TNF receptor superfamily member 25 [Gene - OMIM - HGNC]
  • TNFRSF8:TNF receptor superfamily member 8 [Gene - OMIM - HGNC]
  • TNFRSF9:TNF receptor superfamily member 9 [Gene - OMIM - HGNC]
  • UBIAD1:UbiA prenyltransferase domain containing 1 [Gene - OMIM - HGNC]
  • LOC110121160:VISTA enhancer hs1615 [Gene]
  • LOC110121213:VISTA enhancer hs1833 [Gene]
  • LOC110121258:VISTA enhancer hs2094 [Gene]
  • LOC114827827:VISTA enhancer hs2123 [Gene]
  • LOC110121260:VISTA enhancer hs2125 [Gene]
  • LOC110120623:VISTA enhancer hs241 [Gene]
  • LOC110120648:VISTA enhancer hs289 [Gene]
  • LOC110120666:VISTA enhancer hs389 [Gene]
  • LOC110120672:VISTA enhancer hs408 [Gene]
  • ACOT7:acyl-CoA thioesterase 7 [Gene - OMIM - HGNC]
  • ANGPTL7:angiopoietin like 7 [Gene - OMIM - HGNC]
  • AGTRAP:angiotensin II receptor associated protein [Gene - OMIM - HGNC]
  • RERE:arginine-glutamic acid dipeptide repeats [Gene - OMIM - HGNC]
  • AADACL3:arylacetamide deacetylase like 3 [Gene - HGNC]
  • AADACL4:arylacetamide deacetylase like 4 [Gene - HGNC]
  • CAMTA1:calmodulin binding transcription activator 1 [Gene - OMIM - HGNC]
  • CLSTN1:calsyntenin 1 [Gene - OMIM - HGNC]
  • CA6:carbonic anhydrase 6 [Gene - OMIM - HGNC]
  • CASZ1:castor zinc finger 1 [Gene - OMIM - HGNC]
  • CTNNBIP1:catenin beta interacting protein 1 [Gene - OMIM - HGNC]
  • CENPS:centromere protein S [Gene - OMIM - HGNC]
  • CLCN6:chloride voltage-gated channel 6 [Gene - OMIM - HGNC]
  • CHD5:chromodomain helicase DNA binding protein 5 [Gene - OMIM - HGNC]
  • C1orf127:chromosome 1 open reading frame 127 [Gene - HGNC]
  • C1orf158:chromosome 1 open reading frame 158 [Gene - HGNC]
  • C1orf167:chromosome 1 open reading frame 167 [Gene - HGNC]
  • CORT:cortistatin [Gene - OMIM - HGNC]
  • DHRS3:dehydrogenase/reductase 3 [Gene - OMIM - HGNC]
  • DISP3:dispatched RND transporter family member 3 [Gene - OMIM - HGNC]
  • DRAXIN:dorsal inhibitory axon guidance protein [Gene - OMIM - HGNC]
  • ENO1:enolase 1 [Gene - OMIM - HGNC]
  • ESPN:espin [Gene - OMIM - HGNC]
  • EXOSC10:exosome component 10 [Gene - OMIM - HGNC]
  • HES2:hes family bHLH transcription factor 2 [Gene - OMIM - HGNC]
  • HES3:hes family bHLH transcription factor 3 [Gene - OMIM - HGNC]
  • HNRNPCL1:heterogeneous nuclear ribonucleoprotein C like 1 [Gene - HGNC]
  • H6PD:hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase [Gene - OMIM - HGNC]
  • ICMT:isoprenylcysteine carboxyl methyltransferase [Gene - OMIM - HGNC]
  • KLHL21:kelch like family member 21 [Gene - OMIM - HGNC]
  • KIF1B:kinesin family member 1B [Gene - OMIM - HGNC]
  • LZIC:leucine zipper and CTNNBIP1 domain containing [Gene - OMIM - HGNC]
  • LINC01647:long intergenic non-protein coding RNA 1647 [Gene - HGNC]
  • LINC01672:long intergenic non-protein coding RNA 1672 [Gene - HGNC]
  • LINC01714:long intergenic non-protein coding RNA 1714 [Gene - HGNC]
  • LINC01784:long intergenic non-protein coding RNA 1784 [Gene - HGNC]
  • LINC02606:long intergenic non-protein coding RNA 2606 [Gene - HGNC]
  • LINC02766:long intergenic non-protein coding RNA 2766 [Gene - HGNC]
  • LINC02782:long intergenic non-protein coding RNA 2782 [Gene - HGNC]
  • LINC00337:long intergenic non-protein coding RNA 337 [Gene - HGNC]
  • LNCTAM34A:long non coding transcriptional activator of miR34a [Gene - HGNC]
  • MASP2:mannan binding lectin serine peptidase 2 [Gene - OMIM - HGNC]
  • MTOR:mechanistic target of rapamycin kinase [Gene - OMIM - HGNC]
  • MTHFR:methylenetetrahydrofolate reductase [Gene - OMIM - HGNC]
  • MIR1273D:microRNA 1273d [Gene - HGNC]
  • MIR34A:microRNA 34a [Gene - OMIM - HGNC]
  • MIR4252:microRNA 4252 [Gene - HGNC]
  • MIR4417:microRNA 4417 [Gene - HGNC]
  • MIR4632:microRNA 4632 [Gene - HGNC]
  • MIR4689:microRNA 4689 [Gene - HGNC]
  • MIR5697:microRNA 5697 [Gene - HGNC]
  • MIR6728:microRNA 6728 [Gene - HGNC]
  • MIR6729:microRNA 6729 [Gene - HGNC]
  • MIR6730:microRNA 6730 [Gene - HGNC]
  • MIR7846:microRNA 7846 [Gene - HGNC]
  • MIIP:migration and invasion inhibitory protein [Gene - OMIM - HGNC]
  • MFN2:mitofusin 2 [Gene - OMIM - HGNC]
  • MAD2L2:mitotic arrest deficient 2 like 2 [Gene - OMIM - HGNC]
  • NPPA:natriuretic peptide A [Gene - OMIM - HGNC]
  • NPPB:natriuretic peptide B [Gene - OMIM - HGNC]
  • NPHP4:nephrocystin 4 [Gene - OMIM - HGNC]
  • NMNAT1:nicotinamide nucleotide adenylyltransferase 1 [Gene - OMIM - HGNC]
  • LOC106783575:nonconserved acetylation island sequence 67 enhancer [Gene]
  • NOL9:nucleolar protein 9 [Gene - HGNC]
  • PER3:period circadian regulator 3 [Gene - OMIM - HGNC]
  • PEX14:peroxisomal biogenesis factor 14 [Gene - OMIM - HGNC]
  • PIK3CD:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta [Gene - OMIM - HGNC]
  • PGD:phosphogluconate dehydrogenase [Gene - OMIM - HGNC]
  • PLEKHG5:pleckstrin homology and RhoGEF domain containing G5 [Gene - OMIM - HGNC]
  • KCNAB2:potassium voltage-gated channel subfamily A regulatory beta subunit 2 [Gene - OMIM - HGNC]
  • PLOD1:procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 [Gene - OMIM - HGNC]
  • RBP7:retinol binding protein 7 [Gene - OMIM - HGNC]
  • RPL22:ribosomal protein L22 [Gene - OMIM - HGNC]
  • RNF207:ring finger protein 207 [Gene - OMIM - HGNC]
  • SNORD128:small nucleolar RNA, C/D box 128 [Gene - HGNC]
  • SNORA59A:small nucleolar RNA, H/ACA box 59A [Gene - HGNC]
  • SLC2A5:solute carrier family 2 member 5 [Gene - OMIM - HGNC]
  • SLC2A7:solute carrier family 2 member 7 [Gene - OMIM - HGNC]
  • SLC25A33:solute carrier family 25 member 33 [Gene - OMIM - HGNC]
  • SLC45A1:solute carrier family 45 member 1 [Gene - OMIM - HGNC]
  • SRM:spermidine synthase [Gene - OMIM - HGNC]
  • SPSB1:splA/ryanodine receptor domain and SOCS box containing 1 [Gene - OMIM - HGNC]
  • TAS1R1:taste 1 receptor member 1 [Gene - OMIM - HGNC]
  • TMEM201:transmembrane protein 201 [Gene - HGNC]
  • UBE4B:ubiquitination factor E4B [Gene - OMIM - HGNC]
  • LOC102724450:uncharacterized LOC102724450 [Gene]
  • UTS2:urotensin 2 [Gene - OMIM - HGNC]
  • VPS13D:vacuolar protein sorting 13 homolog D [Gene - OMIM - HGNC]
  • VAMP3:vesicle associated membrane protein 3 [Gene - OMIM - HGNC]
  • ZBTB48:zinc finger and BTB domain containing 48 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
1p36.32-36.21
Genomic location:
Preferred name:
GRCh38/hg38 1p36.32-36.21(chr1:4898439-12911913)x1
HGVS:
  • NC_000001.11:g.(?_4898439)_(12911913_?)del
  • NC_000001.10:g.(?_4958499)_(12971757_?)del
  • NC_000001.9:g.(?_4858359)_(12894344_?)del
Links:
dbVar: nssv1415327; dbVar: nsv817401
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
SCV000177694ISCA site 1

See additional submitters

no assertion criteria providedPathogenic
(Sep 12, 2011)
de novoclinical 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, with clinical assertions as classified by the original submitter.

SCV000177694

Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For data from the original published study, [Kaminsky, et al. 2011|/pubmed/21844811], please see [nstd101|/dbvar/studies/nstd101/].

SCV000177694

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]
PMID:
20466091
PMCID:
PMC2869000

Details of each submission

From ISCA site 1, SCV000177694.4

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

Last Updated: Nov 2, 2019

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