GRCh38/hg38 1p34.3-34.1(chr1:38222737-45636176)x3 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:
RCV000051803.4

Allele description [Variation Report for GRCh38/hg38 1p34.3-34.1(chr1:38222737-45636176)x3]

GRCh38/hg38 1p34.3-34.1(chr1:38222737-45636176)x3

Genes:
  • OXCT2:3-oxoacid CoA-transferase 2 [Gene - OMIM - HGNC]
  • HPDL:4-hydroxyphenylpyruvate dioxygenase like [Gene - HGNC]
  • NT5C1A:5'-nucleotidase, cytosolic IA [Gene - OMIM - HGNC]
  • ATP6V0B:ATPase H+ transporting V0 subunit b [Gene - OMIM - HGNC]
  • BTBD19:BTB domain containing 19 [Gene - HGNC]
  • CTPS1:CTP synthase 1 [Gene - OMIM - HGNC]
  • CITED4:Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4 [Gene - OMIM - HGNC]
  • DMAP1:DNA methyltransferase 1 associated protein 1 [Gene - OMIM - HGNC]
  • DPH2:DPH2 homolog [Gene - OMIM - HGNC]
  • EBNA1BP2:EBNA1 binding protein 2 [Gene - OMIM - HGNC]
  • ELOVL1:ELOVL fatty acid elongase 1 [Gene - OMIM - HGNC]
  • ERI3:ERI1 exoribonuclease family member 3 [Gene - OMIM - HGNC]
  • ERI3-IT1:ERI3 intronic transcript 1 [Gene - HGNC]
  • LOC111464991:GATA motif-containing MPRA enhancers 242 and 247 [Gene]
  • GPBP1L1:GC-rich promoter binding protein 1 like 1 [Gene - HGNC]
  • GJA9-MYCBP:GJA9-MYCBP readthrough [Gene]
  • HECTD3:HECT domain E3 ubiquitin protein ligase 3 [Gene - HGNC]
  • KDM4A-AS1:KDM4A antisense RNA 1 [Gene - HGNC]
  • KIAA0754:KIAA0754 [Gene - HGNC]
  • KLF17:Kruppel like factor 17 [Gene - OMIM - HGNC]
  • KLF18:Kruppel like factor 18 [Gene - HGNC]
  • MPL:MPL proto-oncogene, thrombopoietin receptor [Gene - OMIM - HGNC]
  • MYCBP:MYC binding protein [Gene - OMIM - HGNC]
  • MYCL:MYCL proto-oncogene, bHLH transcription factor [Gene - OMIM - HGNC]
  • NDUFS5:NADH:ubiquinone oxidoreductase subunit S5 [Gene - OMIM - HGNC]
  • NFYC-AS1:NFYC antisense RNA 1 [Gene - HGNC]
  • RNU5D-1:RNA, U5D small nuclear 1 [Gene - HGNC]
  • RNU5F-1:RNA, U5F small nuclear 1 [Gene - HGNC]
  • RRAGC:Ras related GTP binding C [Gene - OMIM - HGNC]
  • SLC2A1-AS1:SLC2A1 antisense RNA 1 [Gene - HGNC]
  • SLFNL1-AS1:SLFNL1 antisense RNA 1 [Gene - HGNC]
  • ST3GAL3:ST3 beta-galactoside alpha-2,3-sialyltransferase 3 [Gene - OMIM - HGNC]
  • SZT2-AS1:SZT2 antisense RNA 1 [Gene - HGNC]
  • SZT2:SZT2, KICSTOR complex subunit [Gene - OMIM - HGNC]
  • SCMH1:Scm polycomb group protein homolog 1 [Gene - OMIM - HGNC]
  • TCTEX1D4:Tctex1 domain containing 4 [Gene - OMIM - HGNC]
  • LOC110120958:VISTA enhancer hs1001 [Gene]
  • LOC110120969:VISTA enhancer hs1031 [Gene]
  • LOC110121002:VISTA enhancer hs1139 [Gene]
  • LOC110121139:VISTA enhancer hs1546 [Gene]
  • LOC110121214:VISTA enhancer hs1857 [Gene]
  • LOC110121256:VISTA enhancer hs2088 [Gene]
  • LOC110120642:VISTA enhancer hs277 [Gene]
  • LOC110120644:VISTA enhancer hs280 [Gene]
  • YBX1:Y-box binding protein 1 [Gene - OMIM - HGNC]
  • ZFP69B:ZFP69 zinc finger protein B [Gene - HGNC]
  • ZFP69:ZFP69 zinc finger protein [Gene - HGNC]
  • AKIRIN1:akirin 1 [Gene - OMIM - HGNC]
  • AKR1A1:aldo-keto reductase family 1 member A1 [Gene - OMIM - HGNC]
  • ARMH1:armadillo-like helical domain containing 1 [Gene - HGNC]
  • ARTN:artemin [Gene - OMIM - HGNC]
  • BEST4:bestrophin 4 [Gene - OMIM - HGNC]
  • B4GALT2:beta-1,4-galactosyltransferase 2 [Gene - OMIM - HGNC]
  • BMP8A:bone morphogenetic protein 8a [Gene - HGNC]
  • BMP8B:bone morphogenetic protein 8b [Gene - OMIM - HGNC]
  • CDC20:cell division cycle 20 [Gene - OMIM - HGNC]
  • C1orf210:chromosome 1 open reading frame 210 [Gene - HGNC]
  • C1orf50:chromosome 1 open reading frame 50 [Gene - HGNC]
  • CFAP57:cilia and flagella associated protein 57 [Gene - OMIM - HGNC]
  • CLDN19:claudin 19 [Gene - OMIM - HGNC]
  • CCDC163:coiled-coil domain containing 163 [Gene - HGNC]
  • CCDC17:coiled-coil domain containing 17 [Gene - HGNC]
  • CCDC24:coiled-coil domain containing 24 [Gene - HGNC]
  • CCDC30:coiled-coil domain containing 30 [Gene - HGNC]
  • COL9A2:collagen type IX alpha 2 chain [Gene - OMIM - HGNC]
  • CAP1:cyclase associated actin cytoskeleton regulatory protein 1 [Gene - OMIM - HGNC]
  • EDN2:endothelin 2 [Gene - OMIM - HGNC]
  • ERMAP:erythroblast membrane associated protein (Scianna blood group) [Gene - OMIM - HGNC]
  • EIF2B3:eukaryotic translation initiation factor 2B subunit gamma [Gene - OMIM - HGNC]
  • EXO5:exonuclease 5 [Gene - HGNC]
  • FAM183A:family with sequence similarity 183 member A [Gene - HGNC]
  • FOXJ3:forkhead box J3 [Gene - OMIM - HGNC]
  • FOXO6:forkhead box O6 [Gene - OMIM - HGNC]
  • GJA9:gap junction protein alpha 9 [Gene - OMIM - HGNC]
  • GUCA2A:guanylate cyclase activator 2A [Gene - OMIM - HGNC]
  • GUCA2B:guanylate cyclase activator 2B [Gene - OMIM - HGNC]
  • HEYL:hes related family bHLH transcription factor with YRPW motif-like [Gene - OMIM - HGNC]
  • HPCAL4:hippocalcin like 4 [Gene - HGNC]
  • HIVEP3:human immunodeficiency virus type I enhancer binding protein 3 [Gene - OMIM - HGNC]
  • HYI:hydroxypyruvate isomerase (putative) [Gene - HGNC]
  • IPO13:importin 13 [Gene - OMIM - HGNC]
  • KIF2C:kinesin family member 2C [Gene - OMIM - HGNC]
  • LINC01144:long intergenic non-protein coding RNA 1144 [Gene - HGNC]
  • LINC01685:long intergenic non-protein coding RNA 1685 [Gene - HGNC]
  • KDM4A:lysine demethylase 4A [Gene - OMIM - HGNC]
  • MFSD2A:major facilitator superfamily domain containing 2A [Gene - OMIM - HGNC]
  • MED8:mediator complex subunit 8 [Gene - OMIM - HGNC]
  • MMACHC:methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria [Gene - OMIM - HGNC]
  • MIR30C1:microRNA 30c-1 [Gene - OMIM - HGNC]
  • MIR30E:microRNA 30e [Gene - HGNC]
  • MIR5584:microRNA 5584 [Gene - HGNC]
  • MIR6079:microRNA 6079 [Gene - HGNC]
  • MIR6733:microRNA 6733 [Gene - HGNC]
  • MIR6734:microRNA 6734 [Gene - HGNC]
  • MIR6735:microRNA 6735 [Gene - HGNC]
  • MACF1:microtubule-actin crosslinking factor 1 [Gene - OMIM - HGNC]
  • MUTYH:mutY DNA glycosylase [Gene - OMIM - HGNC]
  • NASP:nuclear autoantigenic sperm protein [Gene - OMIM - HGNC]
  • NFYC:nuclear transcription factor Y subunit gamma [Gene - OMIM - HGNC]
  • PPT1:palmitoyl-protein thioesterase 1 [Gene - OMIM - HGNC]
  • PTCH2:patched 2 [Gene - OMIM - HGNC]
  • PPIE:peptidylprolyl isomerase E [Gene - OMIM - HGNC]
  • PPIH:peptidylprolyl isomerase H [Gene - OMIM - HGNC]
  • PRDX1:peroxiredoxin 1 [Gene - OMIM - HGNC]
  • PPCS:phosphopantothenoylcysteine synthetase [Gene - OMIM - HGNC]
  • PLK3:polo like kinase 3 [Gene - OMIM - HGNC]
  • PABPC4:poly(A) binding protein cytoplasmic 4 [Gene - OMIM - HGNC]
  • KCNQ4:potassium voltage-gated channel subfamily Q member 4 [Gene - OMIM - HGNC]
  • P3H1:prolyl 3-hydroxylase 1 [Gene - OMIM - HGNC]
  • PTPRF:protein tyrosine phosphatase, receptor type F [Gene - OMIM - HGNC]
  • RLF:rearranged L-myc fusion [Gene - OMIM - HGNC]
  • RIMS3:regulating synaptic membrane exocytosis 3 [Gene - OMIM - HGNC]
  • RHBDL2:rhomboid like 2 [Gene - OMIM - HGNC]
  • RIMKLA:ribosomal modification protein rimK like family member A [Gene - HGNC]
  • RPS8:ribosomal protein S8 [Gene - OMIM - HGNC]
  • RNF220:ring finger protein 220 [Gene - OMIM - HGNC]
  • SLFNL1:schlafen like 1 [Gene - HGNC]
  • SMAP2:small ArfGAP2 [Gene - OMIM - HGNC]
  • SNORD145:small nucleolar RNA, C/D box 145 [Gene - HGNC]
  • SNORD160:small nucleolar RNA, C/D box 160 [Gene - HGNC]
  • SNORD38A:small nucleolar RNA, C/D box 38A [Gene - HGNC]
  • SNORD38B:small nucleolar RNA, C/D box 38B [Gene - HGNC]
  • SNORD46:small nucleolar RNA, C/D box 46 [Gene - HGNC]
  • SNORD55:small nucleolar RNA, C/D box 55 [Gene - HGNC]
  • SNORA110:small nucleolar RNA, H/ACA box 110 [Gene - HGNC]
  • SNORA55:small nucleolar RNA, H/ACA box 55 [Gene - HGNC]
  • SVBP:small vasohibin binding protein [Gene - OMIM - HGNC]
  • SLC2A1:solute carrier family 2 member 1 [Gene - OMIM - HGNC]
  • SLC6A9:solute carrier family 6 member 9 [Gene - OMIM - HGNC]
  • TRIT1:tRNA isopentenyltransferase 1 [Gene - OMIM - HGNC]
  • TOE1:target of EGR1, exonuclease [Gene - OMIM - HGNC]
  • TESK2:testis associated actin remodelling kinase 2 [Gene - OMIM - HGNC]
  • TMCO2:transmembrane and coiled-coil domains 2 [Gene - HGNC]
  • TMEM125:transmembrane protein 125 [Gene - HGNC]
  • TMEM269:transmembrane protein 269 [Gene - HGNC]
  • TMEM53:transmembrane protein 53 [Gene - HGNC]
  • TIE1:tyrosine kinase with immunoglobulin like and EGF like domains 1 [Gene - OMIM - HGNC]
  • LOC101929516:uncharacterized LOC101929516 [Gene]
  • LOC101929536:uncharacterized LOC101929536 [Gene]
  • LOC101929592:uncharacterized LOC101929592 [Gene]
  • LOC101929901:uncharacterized LOC101929901 [Gene]
  • LOC105378663:uncharacterized LOC105378663 [Gene]
  • LOC105378683:uncharacterized LOC105378683 [Gene]
  • LOC339539:uncharacterized LOC339539 [Gene]
  • UROD:uroporphyrinogen decarboxylase [Gene - OMIM - HGNC]
  • ZMYND12:zinc finger MYND-type containing 12 [Gene - HGNC]
  • ZSWIM5:zinc finger SWIM-type containing 5 [Gene - HGNC]
  • ZNF684:zinc finger protein 684 [Gene - HGNC]
  • ZNF691:zinc finger protein 691 [Gene - HGNC]
  • ZMPSTE24:zinc metallopeptidase STE24 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
1p34.3-34.1
Genomic location:
Preferred name:
GRCh38/hg38 1p34.3-34.1(chr1:38222737-45636176)x3
HGVS:
  • NC_000001.11:g.(?_38222737)_(45636176_?)dup
  • NC_000001.10:g.(?_38688409)_(46101848_?)dup
  • NC_000001.9:g.(?_38460996)_(45874435_?)dup
Links:
dbVar: nssv578519; dbVar: nsv530324
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
SCV000079151ISCA site 13

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.

SCV000079151

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 13, SCV000079151.4

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

Last Updated: Mar 30, 2018