NCAPD3 Gene (Protein Coding)

Non-SMC Condensin II Complex Subunit D3

GC11M134150
GIFtS:
42
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]).[su... See more...

Aliases for NCAPD3 Gene

Aliases for NCAPD3 Gene

  • Non-SMC Condensin II Complex Subunit D3 2 3 4 5
  • HCAP-D3 2 3 4
  • Condensin-2 Complex Subunit D3 3 4
  • KIAA0056 2 4
  • CAP-D3 2 3
  • HHCP-6 2 3
  • CAPD3 3 4
  • Hcp-6 2 3
  • Non-SMC Condensin II Complex, Subunit D3 2
  • FLJ42888 2
  • MCPH22 3
  • NCAPD3 5

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 and Primary Autosomal Recessive Microcephaly. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include binding and methylated histone binding. An important paralog of this gene is NCAPD2.

UniProtKB/Swiss-Prot Summary 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 (PubMed:14532007). May promote the resolution of double-strand DNA catenanes (intertwines) between sister chromatids. Condensin-mediated compaction likely increases tension in catenated sister chromatids, providing directionality for type II topoisomerase-mediated strand exchanges toward chromatid decatenation. Specifically required for decatenation of centromeric ultrafine DNA bridges during anaphase. Early in neurogenesis, may play an essential role to ensure accurate mitotic chromosome condensation in neuron stem cells, ultimately affecting neuron pool and cortex size (PubMed:27737959).

Gene Wiki entry for NCAPD3 Gene

Additional gene information for NCAPD3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NCAPD3 Gene

Genomics for NCAPD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for NCAPD3 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NCAPD3

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

Genomic Locations for NCAPD3 Gene

Latest Assembly
chr11:134,150,113-134,225,461
(GRCh38/hg38)
Size:
75,349 bases
Orientation:
Minus strand

Previous Assembly
chr11:134,020,008-134,095,355
(GRCh37/hg19 by Entrez Gene)
Size:
75,348 bases
Orientation:
Minus strand

chr11:134,020,014-134,095,348
(GRCh37/hg19 by Ensembl)
Size:
75,335 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for NCAPD3 Gene

Proteins for NCAPD3 Gene

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

    Protein Symbol:
    P42695-CNDD3_HUMAN
    Recommended name:
    Condensin-2 complex subunit D3
    Protein Accession:
    P42695
    Secondary Accessions:
    • A6NFS2
    • Q4KMQ9

    Protein attributes for NCAPD3 Gene

    Size:
    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

Protein Expression for NCAPD3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for NCAPD3 Gene

  • Ubiquitination at Lys149, Lys442, Lys559, Lys597, Lys618, Lys743, Lys841, Lys929, and Lys1258
  • Modification sites at PhosphoSitePlus

Other Protein References for NCAPD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for NCAPD3
  • Boster Bio Antibodies for NCAPD3

No data available for DME Specific Peptides for NCAPD3 Gene

Domains & Families for NCAPD3 Gene

Gene Families for NCAPD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for NCAPD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NCAPD3 Gene

GenScript: Design optimal peptide antigens:
  • Non-SMC condensin II complex subunit D3 (CNDD3_HUMAN)
  • NCAPD3 protein (Q96FA6_HUMAN)
genes like me logo Genes that share domains with NCAPD3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for NCAPD3 Gene

Function for NCAPD3 Gene

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  6. Cell Lines for research

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 (PubMed:14532007). May promote the resolution of double-strand DNA catenanes (intertwines) between sister chromatids. Condensin-mediated compaction likely increases tension in catenated sister chromatids, providing directionality for type II topoisomerase-mediated strand exchanges toward chromatid decatenation. Specifically required for decatenation of centromeric ultrafine DNA bridges during anaphase. Early in neurogenesis, may play an essential role to ensure accurate mitotic chromosome condensation in neuron stem cells, ultimately affecting neuron pool and cortex size (PubMed:27737959).

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 21873635
GO:0005515 protein binding IPI 17268547
GO:0035064 methylated histone binding IDA 20622854
GO:0042393 histone binding IBA 21873635
genes like me logo Genes that share ontologies with NCAPD3: view

Phenotypes for NCAPD3 Gene

MGI mutant phenotypes for NCAPD3:
inferred from 1 alleles
GenomeRNAi human phenotypes for NCAPD3:
genes like me logo Genes that share phenotypes with NCAPD3: view

Human Phenotype Ontology for NCAPD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NCAPD3

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

Localization for NCAPD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCAPD3 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
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
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NCAPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000779 condensed chromosome, centromeric region IBA 21873635
GO:0000796 condensin complex IBA,IDA 14532007
GO:0000799 nuclear condensin complex IEA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
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
  • Cell cycle_Chromosome condensation in prometaphase
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 IEA,IMP 27737959
GO:0010032 meiotic chromosome condensation IBA 21873635
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

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No Compound Related Data Available

Transcripts for NCAPD3 Gene

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mRNA/cDNA for NCAPD3 Gene

5 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NCAPD3

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: - - -
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:

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: - - -
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8:
SP9:

Relevant External Links for NCAPD3 Gene

GeneLoc Exon Structure for
NCAPD3

Expression for NCAPD3 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

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

mRNA expression in normal human tissues for NCAPD3 Gene
mRNA expression by GTEx for NCAPD3 GenemRNA expression by BioGPS for NCAPD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NCAPD3

SOURCE GeneReport for Unigene cluster for NCAPD3 Gene:

Hs.438550

Evidence on tissue expression from TISSUES for NCAPD3 Gene

  • Nervous system(4.5)
  • Bone marrow(4.2)
  • Skin(2)
genes like me logo Genes that share expression patterns with NCAPD3: view

Primer products for research

No data available for 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
Chimpanzee
(Pan troglodytes)
 Mammalia NCAPD3 30 31
  • 99.35 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia NCAPD3 30 31
  • 84.22 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Ncapd3 30 17 31
  • 79.22 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ncapd3 30
  • 79.07 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 78 (a)
 OneToMany
-- 31
  • 76 (a)
 OneToMany
-- 31
  • 71 (a)
 OneToMany
-- 31
  • 69 (a)
 OneToMany
-- 31
  • 51 (a)
 OneToMany
Cow
(Bos Taurus)
 Mammalia NCAPD3 30 31
  • 72.81 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia NCAPD3 31
  • 70 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves NCAPD3 30 31
  • 65.02 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia NCAPD3 31
  • 56 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia ncapd3 30
  • 61.87 (n)
Zebrafish
(Danio rerio)
 Actinopterygii ncapd3 30 31
  • 56.4 (n)
 OneToOne
zgc55549 30
Worm
(Caenorhabditis elegans)
 Secernentea hcp-6 31
  • 14 (a)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT4G15890 30
  • 43.51 (n)
Rice
(Oryza sativa)
 Liliopsida Os12g0548100 30
  • 44.47 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 32 (a)
 OneToOne
Species where no ortholog for NCAPD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

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

Paralogs for NCAPD3 Gene

Paralogs for NCAPD3 Gene

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

Variants for NCAPD3 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NCAPD3 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
975755 Likely Benign: Intellectual disability 134,168,053(-) ATCT/A
NM_015261.3(NCAPD3):c.3510AGA[1] (p.Glu1171del) 		INFRAME_DELETION
975756 Likely Benign: Intellectual disability 134,217,014(-) T/G
NM_015261.3(NCAPD3):c.304A>C (p.Lys102Gln) 		MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON
975757 Likely Benign: Intellectual disability 134,220,666(-) A/G
NM_015261.3(NCAPD3):c.125T>C (p.Ile42Thr) 		MISSENSE_VARIANT,FIVE_PRIME_UTR
rs116394634 Benign: Intellectual disability; not provided 134,157,939(-) G/A
NM_015261.3(NCAPD3):c.4163C>T (p.Thr1388Met) 		MISSENSE
rs1350194762 Pathogenic: Microcephaly 22, primary, autosomal recessive. Microcephaly 22, primary, autosomal recessive (MCPH22) [MIM:617984] 134,168,111(-) T/Gp.Glu1153Ala
NM_015261.3(NCAPD3):c.3458A>C (p.Glu1153Ala) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NCAPD3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)
NCAPD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NCAPD3

SNP Genotyping and Copy Number Assays for research

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

Disorders for NCAPD3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for NCAPD3 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CNDD3_HUMAN
  • Microcephaly 22, primary, autosomal recessive (MCPH22) [MIM:617984]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. {ECO:0000269 PubMed:27737959}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for NCAPD3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with NCAPD3: view

No data available for Genatlas for NCAPD3 Gene

Publications for NCAPD3 Gene

  1. Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis. (PMID: 27737959) Martin CA … Jackson AP (Genes & development 2016) 3 4 74
  2. 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
  3. 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
  4. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. (PMID: 23728299) Floyd SR … Yaffe MB (Nature 2013) 3 4
  5. 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 41

ExternalLinks

View latest publications for NCAPD3 gene in Mastermind

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