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NC_000001.10:g.4481271_20530242del AND Chromosome 1p36 deletion syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 31, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003159574.1

Allele description [Variation Report for NC_000001.10:g.4481271_20530242del]

NC_000001.10:g.4481271_20530242del

Genes:
  • HTR6:5-hydroxytryptamine receptor 6 [Gene - OMIM - HGNC]
  • ATP13A2:ATPase cation transporting 13A2 [Gene - OMIM - HGNC]
  • CENPS-CORT:CENPS-CORT readthrough [Gene - HGNC]
  • DDI2:DNA damage inducible 1 homolog 2 [Gene - HGNC]
  • DFFA:DNA fragmentation factor subunit alpha [Gene - OMIM - HGNC]
  • DNAJC11:DnaJ heat shock protein family (Hsp40) member C11 [Gene - OMIM - HGNC]
  • DNAJC16:DnaJ heat shock protein family (Hsp40) member C16 [Gene - OMIM - HGNC]
  • EFHD2:EF-hand domain family member D2 [Gene - OMIM - HGNC]
  • ENO1-AS1:ENO1 antisense RNA 1 [Gene - HGNC]
  • EPHA2:EPH receptor A2 [Gene - OMIM - HGNC]
  • EMC1:ER membrane protein complex subunit 1 [Gene - OMIM - HGNC]
  • ERRFI1:ERBB receptor feedback inhibitor 1 [Gene - OMIM - HGNC]
  • FBXO2:F-box protein 2 [Gene - OMIM - HGNC]
  • FBXO42:F-box protein 42 [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]
  • MASP2:MBL associated serine protease 2 [Gene - OMIM - HGNC]
  • MICOS10-NBL1:MICOS10-NBL1 readthrough [Gene - HGNC]
  • MRTO4:MRT4 homolog, ribosome maturation factor [Gene - HGNC]
  • NBL1:NBL1, DAN family BMP antagonist [Gene - OMIM - HGNC]
  • NBPF1:NBPF member 1 [Gene - OMIM - HGNC]
  • NECAP2:NECAP endocytosis associated 2 [Gene - OMIM - HGNC]
  • OTUD3:OTU deubiquitinase 3 [Gene - OMIM - HGNC]
  • PHF13:PHD finger protein 13 [Gene - OMIM - HGNC]
  • PRDM2:PR/SET domain 2 [Gene - OMIM - HGNC]
  • PRAMEF10:PRAME family member 10 [Gene - HGNC]
  • PRAMEF11:PRAME family member 11 [Gene - HGNC]
  • PRAMEF12:PRAME family member 12 [Gene - HGNC]
  • PRAMEF13:PRAME family member 13 [Gene - HGNC]
  • PRAMEF15:PRAME family member 15 [Gene - HGNC]
  • PRAMEF17:PRAME family member 17 [Gene - HGNC]
  • PRAMEF18:PRAME family member 18 [Gene - HGNC]
  • PRAMEF19:PRAME family member 19 [Gene - HGNC]
  • PRAMEF1:PRAME family member 1 [Gene - HGNC]
  • PRAMEF20:PRAME family member 20 [Gene - HGNC]
  • PRAMEF22:PRAME family member 22 [Gene - HGNC]
  • PRAMEF2:PRAME family member 2 [Gene - HGNC]
  • PRAMEF4:PRAME family member 4 [Gene - HGNC]
  • PRAMEF5:PRAME family member 5 [Gene - HGNC]
  • PRAMEF6:PRAME family member 6 [Gene - HGNC]
  • PRAMEF7:PRAME family member 7 [Gene - HGNC]
  • PRAMEF8:PRAME family member 8 [Gene - HGNC]
  • PRAMEF9:PRAME family member 9 [Gene - HGNC]
  • PARK7:Parkinsonism associated deglycase [Gene - OMIM - HGNC]
  • RNU1-4:RNA, U1 small nuclear 4 [Gene - OMIM - HGNC]
  • ARHGEF10L:Rho guanine nucleotide exchange factor 10 like [Gene - OMIM - HGNC]
  • ARHGEF19:Rho guanine nucleotide exchange factor 19 [Gene - OMIM - HGNC]
  • SZRD1:SUZ RNA binding domain containing 1 [Gene - HGNC]
  • 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]
  • UBXN10:UBX domain protein 10 [Gene - OMIM - HGNC]
  • UBIAD1:UbiA prenyltransferase domain containing 1 [Gene - OMIM - HGNC]
  • ACTL8:actin like 8 [Gene - HGNC]
  • ACOT7:acyl-CoA thioesterase 7 [Gene - OMIM - HGNC]
  • AJAP1:adherens junctions associated protein 1 [Gene - OMIM - HGNC]
  • AGMAT:agmatinase [Gene - OMIM - HGNC]
  • ALDH4A1:aldehyde dehydrogenase 4 family member A1 [Gene - OMIM - HGNC]
  • AKR7L:aldo-keto reductase family 7 like (gene/pseudogene) [Gene - OMIM - HGNC]
  • AKR7A2:aldo-keto reductase family 7 member A2 [Gene - OMIM - HGNC]
  • AKR7A3:aldo-keto reductase family 7 member A3 [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]
  • CAPZB:capping actin protein of muscle Z-line subunit beta [Gene - OMIM - HGNC]
  • CA6:carbonic anhydrase 6 [Gene - OMIM - HGNC]
  • CASP9:caspase 9 [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]
  • CLCNKA:chloride voltage-gated channel Ka [Gene - OMIM - HGNC]
  • CLCNKB:chloride voltage-gated channel Kb [Gene - OMIM - HGNC]
  • CHD5:chromodomain helicase DNA binding protein 5 [Gene - OMIM - HGNC]
  • C1orf127:chromosome 1 open reading frame 127 [Gene - OMIM - HGNC]
  • C1orf167:chromosome 1 open reading frame 167 [Gene - HGNC]
  • CTRC:chymotrypsin C [Gene - OMIM - HGNC]
  • CELA2A:chymotrypsin like elastase 2A [Gene - OMIM - HGNC]
  • CELA2B:chymotrypsin like elastase 2B [Gene - OMIM - HGNC]
  • CFAP107:cilia and flagella associated protein 107 [Gene - HGNC]
  • CROCC:ciliary rootlet coiled-coil, rootletin [Gene - OMIM - HGNC]
  • CPLANE2:ciliogenesis and planar polarity effector complex subunit 2 [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]
  • FAM131C:family with sequence similarity 131 member C [Gene - HGNC]
  • FBLIM1:filamin binding LIM protein 1 [Gene - OMIM - HGNC]
  • FHAD1:forkhead associated phosphopeptide binding domain 1 [Gene - HGNC]
  • HSPB7:heat shock protein family B (small) member 7 [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]
  • HNRNPCL2:heterogeneous nuclear ribonucleoprotein C like 2 [Gene - HGNC]
  • H6PD:hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase [Gene - OMIM - HGNC]
  • IGSF21:immunoglobin superfamily member 21 [Gene - HGNC]
  • IFFO2:intermediate filament family orphan 2 [Gene - HGNC]
  • ICMT:isoprenylcysteine carboxyl methyltransferase [Gene - OMIM - HGNC]
  • KAZN:kazrin, periplakin interacting protein [Gene - OMIM - HGNC]
  • KLHDC7A:kelch domain containing 7A [Gene - HGNC]
  • KLHL21:kelch like family member 21 [Gene - OMIM - HGNC]
  • KIF1B:kinesin family member 1B [Gene - OMIM - HGNC]
  • LRRC38:leucine rich repeat containing 38 [Gene - OMIM - HGNC]
  • LZIC:leucine zipper and CTNNBIP1 domain containing [Gene - OMIM - HGNC]
  • LINC01783:long intergenic non-protein coding RNA 1783 [Gene - HGNC]
  • MTOR:mechanistic target of rapamycin kinase [Gene - OMIM - HGNC]
  • MTHFR:methylenetetrahydrofolate reductase [Gene - OMIM - HGNC]
  • MIR34A:microRNA 34a [Gene - OMIM - HGNC]
  • MFAP2:microfibril associated protein 2 [Gene - OMIM - HGNC]
  • MIIP:migration and invasion inhibitory protein [Gene - OMIM - HGNC]
  • MICOS10:mitochondrial contact site and cristae organizing system subunit 10 [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]
  • NOL9:nucleolar protein 9 [Gene - OMIM - HGNC]
  • PAX7:paired box 7 [Gene - OMIM - HGNC]
  • PADI1:peptidyl arginine deiminase 1 [Gene - OMIM - HGNC]
  • PADI2:peptidyl arginine deiminase 2 [Gene - OMIM - HGNC]
  • PADI3:peptidyl arginine deiminase 3 [Gene - OMIM - HGNC]
  • PADI4:peptidyl arginine deiminase 4 [Gene - OMIM - HGNC]
  • PADI6:peptidyl arginine deiminase 6 [Gene - OMIM - 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]
  • PLA2G2A:phospholipase A2 group IIA [Gene - OMIM - HGNC]
  • PLA2G2C:phospholipase A2 group IIC [Gene - HGNC]
  • PLA2G2D:phospholipase A2 group IID [Gene - OMIM - HGNC]
  • PLA2G2E:phospholipase A2 group IIE [Gene - OMIM - HGNC]
  • PLA2G2F:phospholipase A2 group IIF [Gene - OMIM - HGNC]
  • PLA2G5:phospholipase A2 group V [Gene - OMIM - HGNC]
  • PLEKHM2:pleckstrin homology and RUN domain containing M2 [Gene - OMIM - HGNC]
  • PLEKHG5:pleckstrin homology and RhoGEF domain containing G5 [Gene - OMIM - HGNC]
  • PDPN:podoplanin [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]
  • RCC2:regulator of chromosome condensation 2 [Gene - OMIM - HGNC]
  • RSC1A1:regulator of solute carriers 1 [Gene - OMIM - HGNC]
  • RBP7:retinol binding protein 7 [Gene - OMIM - HGNC]
  • RPL22:ribosomal protein L22 [Gene - OMIM - HGNC]
  • RNF186:ring finger protein 186 [Gene - OMIM - HGNC]
  • RNF207:ring finger protein 207 [Gene - OMIM - 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]
  • SLC25A34:solute carrier family 25 member 34 [Gene - OMIM - HGNC]
  • SLC45A1:solute carrier family 45 member 1 [Gene - OMIM - HGNC]
  • SLC66A1:solute carrier family 66 member 1 [Gene - OMIM - HGNC]
  • SPEN:spen family transcriptional repressor [Gene - OMIM - HGNC]
  • SPATA21:spermatogenesis associated 21 [Gene - HGNC]
  • SRM:spermidine synthase [Gene - OMIM - HGNC]
  • SPSB1:splA/ryanodine receptor domain and SOCS box containing 1 [Gene - OMIM - HGNC]
  • SRARP:steroid receptor associated and regulated protein [Gene - OMIM - HGNC]
  • SDHB:succinate dehydrogenase complex iron sulfur subunit B [Gene - OMIM - HGNC]
  • TRQ-CTG14-1:tRNA-Gln (anticodon CTG) 14-1 [Gene - HGNC]
  • TRE-TTC3-1:tRNA-Glu (anticodon TTC) 3-1 [Gene - OMIM - HGNC]
  • TRG-CCC1-1:tRNA-Gly (anticodon CCC) 1-1 [Gene - OMIM - HGNC]
  • TAS1R1:taste 1 receptor member 1 [Gene - OMIM - HGNC]
  • TAS1R2:taste 1 receptor member 2 [Gene - OMIM - HGNC]
  • TMCO4:transmembrane and coiled-coil domains 4 [Gene - HGNC]
  • TMEM201:transmembrane protein 201 [Gene - HGNC]
  • TMEM51:transmembrane protein 51 [Gene - HGNC]
  • TMEM82:transmembrane protein 82 [Gene - HGNC]
  • UBR4:ubiquitin protein ligase E3 component n-recognin 4 [Gene - OMIM - HGNC]
  • UBE4B:ubiquitination factor E4B [Gene - OMIM - HGNC]
  • 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]
  • ZBTB17:zinc finger and BTB domain containing 17 [Gene - OMIM - HGNC]
  • ZBTB48:zinc finger and BTB domain containing 48 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p36.32-36.12
Genomic location:
Chr1: 4481271 - 20530242 (on Assembly GRCh37)
Preferred name:
NC_000001.10:g.4481271_20530242del
HGVS:
NC_000001.10:g.4481271_20530242del
Observations:
1

Condition(s)

Name:
Chromosome 1p36 deletion syndrome (1p36)
Synonyms:
1p36 microdeletion syndrome; 1p36.33 deletion; Monosomy 1p36 syndrome
Identifiers:
MONDO: MONDO:0011929; MeSH: C535362; MedGen: C1842870; Orphanet: 1606; OMIM: 607872

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003853460New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Pathogenic
(Mar 31, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV003853460.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The 1p36.32p36.12 deletion (Chr1:4481271_20530242del) identified here is an interstitial deletion on the short arm of chromosome 1. This 16Mb deletion contains 348 genes, 116 of which are OMIM associated including KCNAB2, RERE, UBE4B, CASZI, PDPN, and SPEN, which are thought to be contributory to the 1p36 deletion syndrome phenotype. Interstitial deletions such as the one identified in this individual are present in approximately 29% of affected individuals with 1p36 deletion syndrome [https://www.ncbi.nlm.nih.gov/books/NBK1191/]].

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Aug 5, 2023