GRCh37/hg19 1p36.3-36.2(chr1:4958499-13178528)x1 AND Global developmental delay

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

Review status:

classified by single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000053724.1

Allele description [Variation Report for GRCh37/hg19 1p36.3-36.2(chr1:4958499-13178528)x1]

Genes:
  • RERE:arginine-glutamic acid dipeptide (RE) repeats [Gene - OMIM]
  • CA6:carbonic anhydrase VI [Gene - OMIM]
  • TNFRSF8:tumor necrosis factor receptor superfamily, member 8 [Gene - OMIM]
  • CLCN6:chloride channel, voltage-sensitive 6 [Gene - OMIM]
  • CORT:cortistatin [Gene - OMIM]
  • DFFA:DNA fragmentation factor, 45kDa, alpha polypeptide [Gene - OMIM]
  • ENO1:enolase 1, (alpha) [Gene - OMIM]
  • MTOR:mechanistic target of rapamycin (serine/threonine kinase) [Gene - OMIM]
  • ZBTB48:zinc finger and BTB domain containing 48 [Gene - OMIM]
  • TNFRSF9:tumor necrosis factor receptor superfamily, member 9 [Gene - OMIM]
  • MTHFR:methylenetetrahydrofolate reductase (NAD(P)H) [Gene - OMIM]
  • NPPA:natriuretic peptide A [Gene - OMIM]
  • NPPB:natriuretic peptide B [Gene - OMIM]
  • PEX14:peroxisomal biogenesis factor 14 [Gene - OMIM]
  • PGD:phosphogluconate dehydrogenase [Gene - OMIM]
  • PIK3CD:phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta [Gene - OMIM]
  • PLOD1:procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 [Gene - OMIM]
  • EXOSC10:exosome component 10 [Gene - OMIM]
  • RPL22:ribosomal protein L22 [Gene - OMIM]
  • SLC2A5:solute carrier family 2 (facilitated glucose/fructose transporter), member 5 [Gene - OMIM]
  • SRM:spermidine synthase [Gene - OMIM]
  • TNFRSF1B:tumor necrosis factor receptor superfamily, member 1B [Gene - OMIM]
  • KCNAB2:potassium voltage-gated channel, shaker-related subfamily, beta member 2 [Gene - OMIM]
  • TNFRSF25:tumor necrosis factor receptor superfamily, member 25 [Gene - OMIM]
  • PER3:period circadian clock 3 [Gene - OMIM]
  • DHRS3:dehydrogenase/reductase (SDR family) member 3 [Gene - OMIM]
  • VAMP3:vesicle-associated membrane protein 3 [Gene - OMIM]
  • H6PD:hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase) [Gene - OMIM]
  • KLHL21:kelch-like family member 21 [Gene]
  • MFN2:mitofusin 2 [Gene - OMIM]
  • ANGPTL7:angiopoietin-like 7 [Gene]
  • UBE4B:ubiquitination factor E4B [Gene - OMIM]
  • MAD2L2:MAD2 mitotic arrest deficient-like 2 (yeast) [Gene - OMIM]
  • MASP2:mannan-binding lectin serine peptidase 2 [Gene - OMIM]
  • UTS2:urotensin 2 [Gene - OMIM]
  • PARK7:parkinson protein 7 [Gene - OMIM]
  • ACOT7:acyl-CoA thioesterase 7 [Gene - OMIM]
  • CLSTN1:calsyntenin 1 [Gene - OMIM]
  • KIF1B:kinesin family member 1B [Gene - OMIM]
  • CAMTA1:calmodulin binding transcription activator 1 [Gene - OMIM]
  • TARDBP:TAR DNA binding protein [Gene - OMIM]
  • ICMT:isoprenylcysteine carboxyl methyltransferase [Gene - OMIM]
  • CHD5:chromodomain helicase DNA binding protein 5 [Gene - OMIM]
  • FBXO2:F-box protein 2 [Gene - OMIM]
  • FBXO6:F-box protein 6 [Gene - OMIM]
  • UBIAD1:UbiA prenyltransferase domain containing 1 [Gene - OMIM]
  • SLC45A1:solute carrier family 45, member 1 [Gene - OMIM]
  • ERRFI1:ERBB receptor feedback inhibitor 1 [Gene - OMIM]
  • HES2:hes family bHLH transcription factor 2 [Gene - OMIM]
  • CASZ1:castor zinc finger 1 [Gene - OMIM]
  • VPS13D:vacuolar protein sorting 13 homolog D (S. cerevisiae) [Gene - OMIM]
  • DNAJC11:DnaJ (Hsp40) homolog, subfamily C, member 11 [Gene - OMIM]
  • CTNNBIP1:catenin, beta interacting protein 1 [Gene - OMIM]
  • AGTRAP:angiotensin II receptor-associated protein [Gene - OMIM]
  • PLEKHG5:pleckstrin homology domain containing, family G (with RhoGef domain) member 5 [Gene - OMIM]
  • PTCHD2:patched domain containing 2 [Gene - OMIM]
  • MIIP:migration and invasion inhibitory protein [Gene - OMIM]
  • NMNAT1:nicotinamide nucleotide adenylyltransferase 1 [Gene - OMIM]
  • PRAMEF1:PRAME family member 1 [Gene]
  • PRAMEF2:PRAME family member 2 [Gene]
  • NOL9:nucleolar protein 9 [Gene]
  • GPR157:G protein-coupled receptor 157 [Gene]
  • SPSB1:splA/ryanodine receptor domain and SOCS box containing 1 [Gene - OMIM]
  • TAS1R1:taste receptor, type 1, member 1 [Gene - OMIM]
  • ESPN:espin [Gene - OMIM]
  • SLC25A33:solute carrier family 25 (pyrimidine nucleotide carrier), member 33 [Gene - OMIM]
  • LZIC:leucine zipper and CTNNBIP1 domain containing [Gene - OMIM]
  • THAP3:THAP domain containing, apoptosis associated protein 3 [Gene - OMIM]
  • C1orf158:chromosome 1 open reading frame 158 [Gene]
  • FBXO44:F-box protein 44 [Gene - OMIM]
  • RBP7:retinol binding protein 7, cellular [Gene - OMIM]
  • AADACL3:arylacetamide deacetylase-like 3 [Gene]
  • C1orf127:chromosome 1 open reading frame 127 [Gene]
  • PHF13:PHD finger protein 13 [Gene]
  • SLC2A7:solute carrier family 2 (facilitated glucose transporter), member 7 [Gene - OMIM]
  • TMEM201:transmembrane protein 201 [Gene]
  • NPHP4:nephronophthisis 4 [Gene - OMIM]
  • C1orf167:chromosome 1 open reading frame 167 [Gene]
  • AADACL4:arylacetamide deacetylase-like 4 [Gene]
  • HNRNPCL1:heterogeneous nuclear ribonucleoprotein C-like 1 [Gene]
  • PRAMEF10:PRAME family member 10 [Gene]
  • DRAXIN:dorsal inhibitory axon guidance protein [Gene - OMIM]
  • APITD1:apoptosis-inducing, TAF9-like domain 1 [Gene - OMIM]
  • GPR153:G protein-coupled receptor 153 [Gene - OMIM]
  • RNF207:ring finger protein 207 [Gene]
  • HES3:hes family bHLH transcription factor 3 [Gene - OMIM]
  • PRAMEF12:PRAME family member 12 [Gene]
  • PRAMEF4:PRAME family member 4 [Gene]
  • MIR34A:microRNA 34a [Gene - OMIM]
  • PRAMEF11:PRAME family member 11 [Gene]
  • PRAMEF6:PRAME family member 6 [Gene]
  • PRAMEF7:PRAME family member 7 [Gene]
  • PRAMEF22:PRAME family member 22 [Gene]
  • ENO1-AS1:ENO1 antisense RNA 1 [Gene]
  • APITD1-CORT:APITD1-CORT readthrough [Gene]
Variant type:
copy number loss
Cytogenetic location:
1p36.3-36.2
Preferred name:
GRCh37/hg19 1p36.3-36.2(chr1:4958499-13178528)x1
HGVS:
NC_000001.10:g.(?_4958499)_(13178528_?)del
Links:
dbVar: nsv532385
Observations:
1

Condition(s)

Name:
Global developmental delay (DD)
Identifiers:
MedGen: C0557874
Prevalence:
Mental retardation is caused by aberrant copy numbers of subtelomeric regions in 3-8% of all cases.

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Assertion and evidence details

Submission AccessionSubmitterReview StatusClinical Significance
(Last evaluated)
OriginMethodConsequenceCitations
SCV000081087International Standards For Cytogenomic Arrays Consortium (ISCA)classified by single submitterPathogenic
(Aug 12, 2011)
not providedclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedAlleles observedFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not 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

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 International Standards For Cytogenomic Arrays Consortium (ISCA), SCV000081087.1

#EthnicityAlleles ObservedChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodVariant allelesAllele frequencyFamiliesCo-occurrences
1not providedyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Jul 18, 2014

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