This gene encodes a member of the barr gene family and a regulatory subunit of the condensin complex. This complex is required for the conversion of interphase chromatin into condensed chromosomes. The protein encoded by this gene is associated with mitotic chromosomes, except during the early phase of chromosome condensation. During interphase, the protein has a distinct punct... See more...

Aliases for NCAPH Gene

Aliases for NCAPH Gene

  • Non-SMC Condensin I Complex Subunit H 2 3 4 5
  • Chromosome-Associated Protein H 3 4
  • Condensin Complex Subunit 2 3 4
  • BRRN1 3 4
  • CAPH 3 4
  • Non-SMC Condensin I Complex, Subunit H 2
  • Barren Homolog 1 (Drosophila) 2
  • Barren (Drosophila) Homolog 2
  • Barren Homolog (Drosophila) 2
  • Barren Homolog Protein 1 4
  • Barren Homolog 1 3
  • XCAP-H Homolog 4
  • KIAA0074 4
  • MCPH23 3
  • HCAP-H 4
  • CAP-H 3
  • BRRN 4

External Ids for NCAPH Gene

Previous HGNC Symbols for NCAPH Gene

  • BRRN1

Previous GeneCards Identifiers for NCAPH Gene

  • GC02P097001
  • GC02P090962

Summaries for NCAPH Gene

Entrez Gene Summary for NCAPH Gene

  • This gene encodes a member of the barr gene family and a regulatory subunit of the condensin complex. This complex is required for the conversion of interphase chromatin into condensed chromosomes. The protein encoded by this gene is associated with mitotic chromosomes, except during the early phase of chromosome condensation. During interphase, the protein has a distinct punctate nucleolar localization. Alternatively spliced transcript variants encoding different proteins have been described. [provided by RefSeq, Jul 2013]

GeneCards Summary for NCAPH Gene

NCAPH (Non-SMC Condensin I Complex Subunit H) is a Protein Coding gene. Diseases associated with NCAPH include Microcephaly 23, Primary, Autosomal Recessive and Microcephaly. Among its related pathways are Aurora B signaling and Cell Cycle, Mitotic.

UniProtKB/Swiss-Prot Summary for NCAPH Gene

  • Regulatory subunit of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes. The condensin complex probably introduces positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerases (PubMed:11136719). 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 NCAPH Gene

Additional gene information for NCAPH Gene

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

Genomics for NCAPH Gene

GeneHancer (GH) Regulatory Elements for NCAPH Gene

Promoters and enhancers for NCAPH Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J096334 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.4 360 3 EP300 ZBTB40 ZNF217 SIN3A NRF1 POLR2G USF1 NCOR1 PHF8 ZFX NCAPH lnc-SNRNP200-2 ITPRIPL1 piR-60051-060
GH02J096304 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.6 -30.0 -30040 2.6 ZBTB40 ZNF217 EP300 SIN3A TCF12 NRF1 MYC POLR2G NCOR1 GTF2E2 SNRNP200 lnc-ITPRIPL1-2 CIAO1 KANSL3 NCAPH ASTL DUSP2
GH02J096263 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.2 -69.9 -69895 4.1 RXRA ZBTB40 ZNF217 EP300 CTCF SIN3A NRF1 POLR2G NCOR1 PHF8 CIAO1 TMEM127 piR-32469 SNRNP200 STARD7-AS1 KANSL3 STARD7 ENSG00000230747 ITPRIPL1 CNNM3
GH02J096233 Enhancer 0.9 Ensembl ENCODE 10.7 -101.6 -101640 2.6 CTCF RAD21 TRIM22 BCL11A SMC3 MEF2B NBN SPI1 SMARCA5 IRF4 lnc-CIAO1-5 lnc-TMEM127-3 piR-58981 STARD7 STARD7-AS1 CIAO1 TMEM127 ADRA2B DUSP2 ASTL
GH02J096236 Enhancer 0.6 Ensembl ENCODE 10.7 -98.7 -98713 0.8 NFIC TFAP4 NFIA BHLHE40 CIAO1 STARD7 STARD7-AS1 TMEM127 ADRA2B ASTL DUSP2 ITPRIPL1 NCAPH ENSG00000230747
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NCAPH on UCSC Golden Path with GeneCards custom track

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

Top Transcription factor binding sites by QIAGEN in the NCAPH gene promoter:
  • AREB6
  • c-Myb
  • E47
  • FOXD1
  • LCR-F1
  • MyoD
  • RP58
  • Tal-1
  • Zic3

Genomic Locations for NCAPH Gene

Genomic Locations for NCAPH Gene
chr2:96,335,741-96,377,095
(GRCh38/hg38)
Size:
41,355 bases
Orientation:
Plus strand
chr2:97,001,484-97,041,274
(GRCh37/hg19)
Size:
39,791 bases
Orientation:
Plus strand

Genomic View for NCAPH Gene

Genes around NCAPH on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NCAPH Gene

Proteins for NCAPH Gene

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

    Protein Symbol:
    Q15003-CND2_HUMAN
    Recommended name:
    Condensin complex subunit 2
    Protein Accession:
    Q15003
    Secondary Accessions:
    • B4E189
    • Q8TB87

    Protein attributes for NCAPH Gene

    Size:
    741 amino acids
    Molecular mass:
    82563 Da
    Quaternary structure:
    • Component of the condensin complex, which contains the SMC2 and SMC4 heterodimer, and three non SMC subunits that probably regulate the complex: NCAPH/BRRN1, NCAPD2/CAPD2 and NCAPG.
    SequenceCaution:
    • Sequence=BAA07556.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NCAPH Gene

    Alternative splice isoforms for NCAPH Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NCAPH Gene

Post-translational modifications for NCAPH Gene

  • Phosphorylated by CDK1. Its phosphorylation, as well as that of NCAPD2 and NCAPG subunits, activates the condensin complex and is required for chromosome condensation (By similarity).
  • Ubiquitination at Lys41, Lys394, Lys424, Lys495, and Lys648
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NCAPH Gene

Domains & Families for NCAPH Gene

Gene Families for NCAPH Gene

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

Protein Domains for NCAPH Gene

Blocks:
  • Barren
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NCAPH Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51440, highly similar to Condensin complex subunit 2 (B4E189_HUMAN)
  • XCAP-H homolog (CND2_HUMAN)
  • Condensin complex subunit 2 (E9PHA2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q15003

UniProtKB/Swiss-Prot:

CND2_HUMAN :
  • Belongs to the CND2 (condensin subunit 2) family.
Family:
  • Belongs to the CND2 (condensin subunit 2) family.
genes like me logo Genes that share domains with NCAPH: view

Function for NCAPH Gene

Molecular function for NCAPH Gene

UniProtKB/Swiss-Prot Function:
Regulatory subunit of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes. The condensin complex probably introduces positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerases (PubMed:11136719). 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 NCAPH Gene

Gene Ontology (GO) - Molecular Function for NCAPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IBA 21873635
GO:0005515 protein binding IPI 17268547
GO:0044547 DNA topoisomerase binding IBA 21873635
GO:0072587 DNA topoisomerase (ATP-hydrolyzing) activator activity IBA 21873635
genes like me logo Genes that share ontologies with NCAPH: view
genes like me logo Genes that share phenotypes with NCAPH: view

Human Phenotype Ontology for NCAPH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NCAPH Gene

MGI Knock Outs for NCAPH:
  • Ncaph Ncaph<tm1.2Itl>
  • Ncaph Ncaph<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

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

Localization for NCAPH Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCAPH Gene

Nucleus. Cytoplasm. Chromosome. Note=In interphase cells, the majority of the condensin complex is found in the cytoplasm, while a minority of the complex is associated with chromatin. A subpopulation of the complex however remains associated with chromosome foci in interphase cells. During mitosis, most of the condensin complex is associated with the chromatin. At the onset of prophase, the regulatory subunits of the complex are phosphorylated by CDK1, leading to condensin's association with chromosome arms and to chromosome condensation. Dissociation from chromosomes is observed in late telophase.

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 NCAPH gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for NCAPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000796 condensin complex IDA 11136719
GO:0000799 nuclear condensin complex IBA 21873635
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with NCAPH: view

Pathways & Interactions for NCAPH Gene

PathCards logo

SuperPathways for NCAPH Gene

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

Pathways by source for NCAPH Gene

1 BioSystems pathway for NCAPH Gene
1 GeneGo (Thomson Reuters) pathway for NCAPH Gene
  • Cell cycle_Chromosome condensation in prometaphase

Gene Ontology (GO) - Biological Process for NCAPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007049 cell cycle IEA --
GO:0007076 mitotic chromosome condensation IEA,IMP 27737959
GO:0007143 female meiotic nuclear division IEA --
GO:0010032 meiotic chromosome condensation IEA --
GO:0030261 chromosome condensation IEA --
genes like me logo Genes that share ontologies with NCAPH: view

No data available for SIGNOR curated interactions for NCAPH Gene

Drugs & Compounds for NCAPH Gene

No Compound Related Data Available

Transcripts for NCAPH Gene

mRNA/cDNA for NCAPH Gene

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

CRISPR Products

Inhibitory RNA Products

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

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

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^
SP1: -
SP2: - - - - - - - - - - -
SP3: - -
SP4: - - -
SP5: -
SP6: - - - -
SP7:
SP8: - - -

ExUns: 16 ^ 17 ^ 18a · 18b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for NCAPH Gene

GeneLoc Exon Structure for
NCAPH

Expression for NCAPH Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NCAPH Gene

This gene is overexpressed in Testis (x9.8).

Protein differential expression in normal tissues from HIPED for NCAPH Gene

This gene is overexpressed in Bone (28.1), Lung (10.3), Platelet (7.5), and Testis (6.3).

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



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

SOURCE GeneReport for Unigene cluster for NCAPH Gene:

Hs.308045

mRNA Expression by UniProt/SwissProt for NCAPH Gene:

Q15003-CND2_HUMAN
Tissue specificity: Widely expressed at low level. Expressed in proliferating cells.

Evidence on tissue expression from TISSUES for NCAPH Gene

  • Bone marrow(4.2)
  • Kidney(4)
  • Pancreas(3.1)
  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with NCAPH: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NCAPH Gene

Orthologs for NCAPH Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NCAPH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NCAPH 31 30
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NCAPH 31 30
  • 86.93 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NCAPH 31 30
  • 83.63 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ncaph 17 31 30
  • 81.74 (n)
oppossum
(Monodelphis domestica)
Mammalia NCAPH 31
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NCAPH 31
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves NCAPH 31 30
  • 65.96 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NCAPH 31
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ncaph 30
  • 62.69 (n)
Str.10092 30
African clawed frog
(Xenopus laevis)
Amphibia brrn1-prov 30
zebrafish
(Danio rerio)
Actinopterygii ncaph 31 30
  • 58.51 (n)
OneToOne
wufc69h06 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7620 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011508 30
  • 44.06 (n)
fruit fly
(Drosophila melanogaster)
Insecta barr 31 30
  • 41.75 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BRN1 33 31
  • 20 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5013 31
  • 42 (a)
OneToOne
Species where no ortholog for NCAPH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NCAPH Gene

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

Paralogs for NCAPH Gene

No data available for Paralogs for NCAPH Gene

Variants for NCAPH Gene

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

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
716739 Benign: not provided 96,344,170(+) A/G MISSENSE_VARIANT
730784 Likely Benign: not provided 96,367,346(+) G/A SYNONYMOUS_VARIANT
745992 Likely Benign: not provided 96,365,868(+) T/C INTRON_VARIANT
769568 Benign: not provided 96,353,406(+) A/G INTRON_VARIANT
773426 Likely Benign: not provided 96,354,330(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for NCAPH Gene

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

Variant ID Type Subtype PubMed ID
dgv607e201 CNV deletion 23290073
esv3425717 CNV duplication 20981092
esv3591652 OTHER inversion 21293372
esv5003 OTHER complex 18987735
nsv1135873 CNV deletion 24896259
nsv508155 CNV deletion 20534489
nsv819311 CNV loss 19587683
nsv834305 CNV gain 17160897

Variation tolerance for NCAPH Gene

Residual Variation Intolerance Score: 34% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.12; 51.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NCAPH Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NCAPH Gene

MalaCards: The human disease database

(3) MalaCards diseases for NCAPH Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microcephaly 23, primary, autosomal recessive
  • mcph23
microcephaly
  • microcephalus
ovary serous adenocarcinoma
  • malignant ovarian serous tumor
- elite association - COSMIC cancer census association via MalaCards
Search NCAPH in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CND2_HUMAN
  • Microcephaly 23, primary, autosomal recessive (MCPH23) [MIM:617985]: 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 mutations affecting the gene represented in this entry.

Additional Disease Information for NCAPH

genes like me logo Genes that share disorders with NCAPH: view

No data available for Genatlas for NCAPH Gene

Publications for NCAPH 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 54
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  3. Cell cycle-dependent expression and nucleolar localization of hCAP-H. (PMID: 11694586) Cabello OA … Belmont JW (Molecular biology of the cell 2001) 3 4 54
  4. Chromosome condensation by a human condensin complex in Xenopus egg extracts. (PMID: 11136719) Kimura K … Hirano T (The Journal of biological chemistry 2001) 3 4 54
  5. Localization of BRRN1, the human homologue of Drosophila barr, to 2q11.2. (PMID: 9417923) Cabello OA … Belmont JW (Genomics 1997) 2 3 54

Products for NCAPH Gene

Sources for NCAPH Gene