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Aliases for NCAPD3 Gene

Aliases for NCAPD3 Gene

  • Non-SMC Condensin II Complex Subunit D3 2 3 4 5
  • HCAP-D3 3 4
  • CAPD3 3 4
  • Non-SMC Condensin II Complex, Subunit D3 2
  • Condensin-2 Complex Subunit D3 3
  • KIAA0056 4
  • CAP-D3 3
  • MCPH22 3
  • HHCP-6 3
  • Hcp-6 3

External Ids for NCAPD3 Gene

Previous GeneCards Identifiers for NCAPD3 Gene

  • GC11M133529
  • GC11M134022
  • GC11M129976

Summaries for NCAPD3 Gene

Entrez Gene Summary for NCAPD3 Gene

  • Condensin complexes I and II play essential roles in mitotic chromosome assembly and segregation. Both condensins contain 2 invariant structural maintenance of chromosome (SMC) subunits, SMC2 (MIM 605576) and SMC4 (MIM 605575), but they contain different sets of non-SMC subunits. NCAPD3 is 1 of 3 non-SMC subunits that define condensin II (Ono et al., 2003 [PubMed 14532007]).[supplied by OMIM, Mar 2008]

GeneCards Summary for NCAPD3 Gene

NCAPD3 (Non-SMC Condensin II Complex Subunit D3) is a Protein Coding gene. Diseases associated with NCAPD3 include Microcephaly 22, Primary, Autosomal Recessive. Among its related pathways are Cell Cycle, Mitotic and Cell cycle_Chromosome condensation in prometaphase. Gene Ontology (GO) annotations related to this gene include binding and methylated histone binding.

UniProtKB/Swiss-Prot for NCAPD3 Gene

  • Regulatory subunit of the condensin-2 complex, a complex which establishes mitotic chromosome architecture and is involved in physical rigidity of the chromatid axis.

Gene Wiki entry for NCAPD3 Gene

Additional gene information for NCAPD3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NCAPD3 Gene

Genomics for NCAPD3 Gene

GeneHancer (GH) Regulatory Elements for NCAPD3 Gene

Promoters and enhancers for NCAPD3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J134222 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 667.1 +1.0 958 3 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B NCAPD3 VPS26B GC11P134223 ACAD8 JAM3 GLB1L3
GH11J134068 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 16.7 +153.3 153340 7.4 KLF17 MZF1 SIN3A BMI1 ZNF2 YY1 ZNF335 SCRT2 RCOR1 ZBTB2 JAM3 NCAPD3 ACAD8 IGSF9B LOC100533644 ENSG00000255348 VPS26B THYN1 GC11P134081
GH11J134118 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 17.1 +104.9 104862 4.7 GATA3 POLR2A IKZF1 JUN NFE2 FOS NCAPD3 JAM3 LOC100533644 ENSG00000255348 IGSF9B GLB1L3 THYN1 GC11M134124 GC11P134081
GH11J134139 Enhancer 1 Ensembl ENCODE dbSUPER 17.7 +85.5 85523 1.2 CTCF ZNF654 REST RAD21 TEAD3 SMC3 ZNF143 RCOR1 PRDM1 PIR32251 JAM3 NCAPD3 LOC100533644 ENSG00000255348 VPS26B IGSF9B GLB1L3 THYN1 GC11P134146
GH11J134715 Enhancer 0.6 dbSUPER 26.5 -492.6 -492581 4.9 ZNF146 ZBTB11 ZFP64 ZNF140 ZC3H11A REST ZNF623 ZNF781 ZNF518A ZNF697 NCAPD3 THYN1 LOC105369584 ENSG00000251226
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NCAPD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NCAPD3 gene promoter:
  • COMP1
  • POU2F1a
  • POU2F1
  • c-Myb
  • HNF-4alpha1
  • Pax-2
  • Pax-2a
  • HNF-4alpha2
  • MAZR
  • c-Myc

Genomic Locations for NCAPD3 Gene

Genomic Locations for NCAPD3 Gene
75,336 bases
Minus strand
75,335 bases
Minus strand

Genomic View for NCAPD3 Gene

Genes around NCAPD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NCAPD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NCAPD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NCAPD3 Gene

Proteins for NCAPD3 Gene

  • Protein details for NCAPD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Condensin-2 complex subunit D3
    Protein Accession:
    Secondary Accessions:
    • A6NFS2
    • Q4KMQ9

    Protein attributes for NCAPD3 Gene

    1498 amino acids
    Molecular mass:
    168891 Da
    Quaternary structure:
    • Component of the condensin-2 complex, which contains the SMC2 and SMC4 heterodimer, and 3 non SMC subunits that probably regulate the complex: NCAPH2, NCAPD3 and NCAPG2. Interacts with BRD4 (isoform B), leading to insulate chromatin from DNA damage response pathway.

neXtProt entry for NCAPD3 Gene

Post-translational modifications for NCAPD3 Gene

  • Ubiquitination at isoforms=1258, isoforms=929, isoforms=841, Lys743, isoforms=618, Lys597, Lys559, isoforms=442, and isoforms=149
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NCAPD3 Gene

Domains & Families for NCAPD3 Gene

Gene Families for NCAPD3 Gene

Protein Domains for NCAPD3 Gene

Suggested Antigen Peptide Sequences for NCAPD3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NCAPD3: view

No data available for UniProtKB/Swiss-Prot for NCAPD3 Gene

Function for NCAPD3 Gene

Molecular function for NCAPD3 Gene

UniProtKB/Swiss-Prot Function:
Regulatory subunit of the condensin-2 complex, a complex which establishes mitotic chromosome architecture and is involved in physical rigidity of the chromatid axis.

Phenotypes From GWAS Catalog for NCAPD3 Gene

Gene Ontology (GO) - Molecular Function for NCAPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IBA --
GO:0005488 binding IEA --
GO:0005515 protein binding IPI 17268547
GO:0035064 methylated histone binding IDA 20622854
GO:0042393 histone binding IBA --
genes like me logo Genes that share ontologies with NCAPD3: view

Phenotypes for NCAPD3 Gene

genes like me logo Genes that share phenotypes with NCAPD3: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NCAPD3 Gene

Localization for NCAPD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCAPD3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NCAPD3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NCAPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000779 condensed chromosome, centromeric region IBA --
GO:0000799 nuclear condensin complex IDA 14532007
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with NCAPD3: view

Pathways & Interactions for NCAPD3 Gene

genes like me logo Genes that share pathways with NCAPD3: view

Pathways by source for NCAPD3 Gene

1 GeneGo (Thomson Reuters) pathway for NCAPD3 Gene
2 Cell Signaling Technology pathways for NCAPD3 Gene

Gene Ontology (GO) - Biological Process for NCAPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007049 cell cycle IEA --
GO:0007076 mitotic chromosome condensation IDA,IEA 14532007
GO:0010032 meiotic chromosome condensation IBA --
GO:0030261 chromosome condensation IEA --
GO:0051301 cell division IEA --
genes like me logo Genes that share ontologies with NCAPD3: view

No data available for SIGNOR curated interactions for NCAPD3 Gene

Drugs & Compounds for NCAPD3 Gene

No Compound Related Data Available

Transcripts for NCAPD3 Gene

mRNA/cDNA for NCAPD3 Gene

Unigene Clusters for NCAPD3 Gene

Non-SMC condensin II complex, subunit D3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NCAPD3 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^
SP1: - -
SP2: - -
SP3: - - -
SP7: -

ExUns: 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29a · 29b ^ 30 ^ 31 ^ 32 ^ 33 ^ 34a · 34b ^ 35a · 35b ^ 36 ^ 37 ^ 38 ^ 39a · 39b
SP1: - - - -
SP2: - - -
SP5: -

Relevant External Links for NCAPD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NCAPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NCAPD3 Gene

Protein differential expression in normal tissues from HIPED for NCAPD3 Gene

This gene is overexpressed in Breast (37.2), Spleen (13.4), Lung (9.5), and Ovary (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NCAPD3 Gene

Protein tissue co-expression partners for NCAPD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of NCAPD3 Gene:


SOURCE GeneReport for Unigene cluster for NCAPD3 Gene:


Evidence on tissue expression from TISSUES for NCAPD3 Gene

  • Nervous system(4.3)
  • Bone marrow(4.2)
genes like me logo Genes that share expression patterns with NCAPD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NCAPD3 Gene

Orthologs for NCAPD3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NCAPD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NCAPD3 34 33
  • 99.35 (n)
(Canis familiaris)
Mammalia NCAPD3 34 33
  • 84.22 (n)
(Mus musculus)
Mammalia Ncapd3 16 34 33
  • 79.22 (n)
(Rattus norvegicus)
Mammalia Ncapd3 33
  • 79.07 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 78 (a)
-- 34
  • 76 (a)
-- 34
  • 71 (a)
-- 34
  • 69 (a)
-- 34
  • 51 (a)
(Bos Taurus)
Mammalia NCAPD3 34 33
  • 72.81 (n)
(Monodelphis domestica)
Mammalia NCAPD3 34
  • 70 (a)
(Gallus gallus)
Aves NCAPD3 34 33
  • 65.02 (n)
(Anolis carolinensis)
Reptilia NCAPD3 34
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ncapd3 33
  • 61.87 (n)
(Danio rerio)
Actinopterygii ncapd3 34 33
  • 56.4 (n)
zgc55549 33
(Caenorhabditis elegans)
Secernentea hcp-6 34
  • 14 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G15890 33
  • 43.51 (n)
(Oryza sativa)
Liliopsida Os12g0548100 33
  • 44.47 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 32 (a)
Species where no ortholog for NCAPD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NCAPD3 Gene

Gene Tree for NCAPD3 (if available)
Gene Tree for NCAPD3 (if available)
Evolutionary constrained regions (ECRs) for NCAPD3: view image

Paralogs for NCAPD3 Gene

No data available for Paralogs for NCAPD3 Gene

Variants for NCAPD3 Gene

Sequence variations from dbSNP and Humsavar for NCAPD3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs142896286 likely-benign, not specified 134,210,453(-) G/A 5_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1000040961 -- 134,154,480(-) /G intron_variant
rs1000041907 -- 134,217,190(-) A/T intron_variant
rs1000042481 -- 134,152,110(-) G/A/C downstream_transcript_variant
rs1000073378 -- 134,170,118(-) G/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NCAPD3 Gene

Variant ID Type Subtype PubMed ID
esv2745322 CNV deletion 23290073
esv28602 CNV loss 19812545
esv3579992 CNV loss 25503493
esv3892114 CNV gain 25118596
nsv521581 CNV gain 19592680
nsv826147 CNV gain 20364138
nsv832299 CNV loss 17160897
nsv952767 CNV deletion 24416366

Variation tolerance for NCAPD3 Gene

Residual Variation Intolerance Score: 22.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.41; 63.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NCAPD3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NCAPD3 Gene

Disorders for NCAPD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NCAPD3 Gene - From: OMIM and ClinVar

Disorder Aliases PubMed IDs
microcephaly 22, primary, autosomal recessive
  • mcph22
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for NCAPD3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NCAPD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NCAPD3 Gene

Publications for NCAPD3 Gene

  1. Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. (PMID: 14532007) Ono T … Hirano T (Cell 2003) 2 3 4 58
  2. Prediction of the coding sequences of unidentified human genes. II. The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 7584044) Nomura N … Tabata S (DNA research : an international journal for rapid publication of reports on genes and genomes 1994) 2 3 4 58
  3. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. (PMID: 23728299) Floyd SR … Yaffe MB (Nature 2013) 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. (PMID: 17903297) Seshadri S … Wolf PA (BMC medical genetics 2007) 3 44 58

Products for NCAPD3 Gene

Sources for NCAPD3 Gene

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