Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	23310
Gene name	Non-SMC condensin II complex subunit D3
Gene symbol	NCAPD3
Synonyms (NCBI Gene)	CAP-D3CAPD3MCPH22hCAP-D3hHCP-6hcp-6
Chromosome	11
Chromosome location	11q25
Summary	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

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1350194762	T>C,G	Pathogenic	Missense variant, coding sequence variant
rs1555139372	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1555143325	T>C	Pathogenic	Intron variant

Show/Hide all (82)

miRTarBase ID	miRNA	Experiments	Reference
MIRT023702	hsa-miR-1-3p	Proteomics	18668040
MIRT045217	hsa-miR-186-5p	CLASH	23622248
MIRT044595	hsa-miR-320a	CLASH	23622248
MIRT525944	hsa-miR-6715a-3p	PAR-CLIP	22012620
MIRT525942	hsa-miR-6729-3p	PAR-CLIP	22012620
MIRT525943	hsa-miR-361-3p	PAR-CLIP	22012620
MIRT525944	hsa-miR-6715a-3p	PAR-CLIP	22012620
MIRT525942	hsa-miR-6729-3p	PAR-CLIP	22012620
MIRT525943	hsa-miR-361-3p	PAR-CLIP	22012620
MIRT1175787	hsa-miR-105	CLIP-seq
MIRT1175788	hsa-miR-142-5p	CLIP-seq
MIRT1175789	hsa-miR-3197	CLIP-seq
MIRT1175790	hsa-miR-338-5p	CLIP-seq
MIRT1175791	hsa-miR-3671	CLIP-seq
MIRT1175792	hsa-miR-3689a-3p	CLIP-seq
MIRT1175793	hsa-miR-3689c	CLIP-seq
MIRT1175794	hsa-miR-4456	CLIP-seq
MIRT1175795	hsa-miR-4638-3p	CLIP-seq
MIRT1175796	hsa-miR-4694-3p	CLIP-seq
MIRT1175797	hsa-miR-4728-5p	CLIP-seq
MIRT1175798	hsa-miR-541	CLIP-seq
MIRT1175799	hsa-miR-561	CLIP-seq
MIRT1175800	hsa-miR-607	CLIP-seq
MIRT1175801	hsa-miR-654-5p	CLIP-seq
MIRT1175787	hsa-miR-105	CLIP-seq
MIRT2050907	hsa-miR-125a-5p	CLIP-seq
MIRT2050908	hsa-miR-125b	CLIP-seq
MIRT2050909	hsa-miR-28-5p	CLIP-seq
MIRT2050910	hsa-miR-3117-5p	CLIP-seq
MIRT2050911	hsa-miR-3120-3p	CLIP-seq
MIRT2050912	hsa-miR-3139	CLIP-seq
MIRT2050913	hsa-miR-3150b-3p	CLIP-seq
MIRT2050914	hsa-miR-3154	CLIP-seq
MIRT1175791	hsa-miR-3671	CLIP-seq
MIRT2050915	hsa-miR-3675-3p	CLIP-seq
MIRT2050916	hsa-miR-3676	CLIP-seq
MIRT2050917	hsa-miR-3692	CLIP-seq
MIRT2050918	hsa-miR-4319	CLIP-seq
MIRT2050919	hsa-miR-4645-3p	CLIP-seq
MIRT2050920	hsa-miR-4689	CLIP-seq
MIRT1175796	hsa-miR-4694-3p	CLIP-seq
MIRT2050921	hsa-miR-4755-3p	CLIP-seq
MIRT2050922	hsa-miR-4784	CLIP-seq
MIRT2050923	hsa-miR-4795-3p	CLIP-seq
MIRT2050924	hsa-miR-485-3p	CLIP-seq
MIRT2050925	hsa-miR-487a	CLIP-seq
MIRT2050926	hsa-miR-499-3p	CLIP-seq
MIRT2050927	hsa-miR-499a-3p	CLIP-seq
MIRT2050928	hsa-miR-514	CLIP-seq
MIRT2050929	hsa-miR-514b-3p	CLIP-seq
MIRT2050930	hsa-miR-544b	CLIP-seq
MIRT1175800	hsa-miR-607	CLIP-seq
MIRT2050931	hsa-miR-708	CLIP-seq
MIRT2050932	hsa-miR-765	CLIP-seq
MIRT2279998	hsa-miR-1297	CLIP-seq
MIRT2279999	hsa-miR-26a	CLIP-seq
MIRT2280000	hsa-miR-26b	CLIP-seq
MIRT2280001	hsa-miR-3153	CLIP-seq
MIRT2050915	hsa-miR-3675-3p	CLIP-seq
MIRT2280002	hsa-miR-4465	CLIP-seq
MIRT2050919	hsa-miR-4645-3p	CLIP-seq
MIRT2280003	hsa-miR-4668-5p	CLIP-seq
MIRT2050923	hsa-miR-4795-3p	CLIP-seq
MIRT2050928	hsa-miR-514	CLIP-seq
MIRT2050929	hsa-miR-514b-3p	CLIP-seq
MIRT2391412	hsa-miR-1254	CLIP-seq
MIRT2391413	hsa-miR-1976	CLIP-seq
MIRT2391414	hsa-miR-3116	CLIP-seq
MIRT2050915	hsa-miR-3675-3p	CLIP-seq
MIRT2391415	hsa-miR-3690	CLIP-seq
MIRT1175795	hsa-miR-4638-3p	CLIP-seq
MIRT2050919	hsa-miR-4645-3p	CLIP-seq
MIRT2391416	hsa-miR-4722-3p	CLIP-seq
MIRT2391417	hsa-miR-4763-5p	CLIP-seq
MIRT2050923	hsa-miR-4795-3p	CLIP-seq
MIRT2050924	hsa-miR-485-3p	CLIP-seq
MIRT2050925	hsa-miR-487a	CLIP-seq
MIRT2050926	hsa-miR-499-3p	CLIP-seq
MIRT2050927	hsa-miR-499a-3p	CLIP-seq
MIRT2050928	hsa-miR-514	CLIP-seq
MIRT2050929	hsa-miR-514b-3p	CLIP-seq
MIRT2391418	hsa-miR-661	CLIP-seq

Show/Hide all (29)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000280	Process	Nuclear division	IEA
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000779	Component	Condensed chromosome, centromeric region	IBA
GO:0000794	Component	Condensed nuclear chromosome	ISO
GO:0000796	Component	Condensin complex	IBA
GO:0000796	Component	Condensin complex	IDA	14532007
GO:0000796	Component	Condensin complex	IEA
GO:0000796	Component	Condensin complex	NAS	17268547
GO:0005515	Function	Protein binding	IPI	17268547, 23728299, 26496610, 29028794, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005721	Component	Pericentric heterochromatin	IDA	20551165
GO:0006325	Process	Chromatin organization	IEA
GO:0007076	Process	Mitotic chromosome condensation	IBA
GO:0007076	Process	Mitotic chromosome condensation	IDA	14532007
GO:0007076	Process	Mitotic chromosome condensation	IEA
GO:0007076	Process	Mitotic chromosome condensation	IMP	27737959
GO:0010032	Process	Meiotic chromosome condensation	IBA
GO:0016020	Component	Membrane	HDA	19946888
GO:0030261	Process	Chromosome condensation	IEA
GO:0031981	Component	Nuclear lumen	IEA
GO:0042393	Function	Histone binding	IBA
GO:0051301	Process	Cell division	IEA
GO:0051984	Process	Positive regulation of chromosome segregation	ISO
GO:0098813	Process	Nuclear chromosome segregation	IEA
GO:0140117	Function	Histone H4K20me1 reader activity	IDA	20622854
GO:1905820	Process	Positive regulation of chromosome separation	ISO
GO:1905821	Process	Positive regulation of chromosome condensation	ISS

MIM	HGNC	e!Ensembl
609276	28952	ENSG00000151503

P42695

Protein name

Condensin-2 complex subunit D3 (Non-SMC condensin II complex subunit D3) (hCAP-D3)

Protein 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 (i

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF12717	Cnd1	956 → 1134	non-SMC mitotic condensation complex subunit 1	Family

Sequence

MVALRGLGSGLQPWCPLDLRLEWVDTVWELDFTETEPLDPSIEAEIIETGLAAFTKLYES
LLPFATGEHGSMESIWTFFIENNVSHSTLVALFYHFVQIVHKKNVSVQYREYGLHAAGLY
FLLLEVPGSVANQVFHPVMFDKCIQTLKKSWPQESNLNRKRKKEQPKSSQANPGRHRKRG
KPPRREDIEMDEIIEEQEDENICFSARDLSQIRNAIFHLLKNFLRLLPKFSLKEKPQCVQ
NCIEVFVSLTNFEPVLHECHVTQARALNQAKYIPELAYYGLYLLCSPIHGEGDKVISCVF
HQMLSVILMLEVGEGSHRAPLAVTSQVINCRNQAVQFISALVDELKESIFPVVRILLQHI
CAKVVDKSEYRTFAAQSLVQLLSKLPCGEYAMFIAWLYKYSRSSKIPHRVFTLDVVLALL
ELPEREVDNTLSLEHQKFLKHKFLVQEIMFDRCLDKAPTVRSKALSSFAHCLELTVTSAS
ESILELLINSPTFSVIESHPGTLLRNSSAFSYQRQTSNRSEPSGEINIDSSGETVGSGER
CVMAMLRRRIRDEKTNVRKSALQVLVSILKHCDVSGMKEDLWILQDQCRDPAVSVRKQAL
QSLTELLMAQPRCVQIQKAWLRGVVPVVMDCESTVQEKALEFLDQLLLQNIRHHSHFHSG
DDSQVLAWALLTLLTTESQELSRYLNKAFHIWSKKEKFSPTFINNVISHTGTEHSAPAWM
LLSKIAGSSPRLDYSRIIQSWEKISSQQNPNSNTLGHILCVIGHIAKHLPKSTRDKVTDA
VKCKLNGFQWSLEVISSAVDALQRLCRASAETPAEEQELLTQVCGDVLSTCEHRLSNIVL
KENGTGNMDEDLLVKYIFTLGDIAQLCPARVEKRIFLLIQSVLASSADADHSPSSQGSSE
APASQPPPQVRGSVMPSVIRAHAIITLGKLCLQHEDLAKKSIPALVRELEVCEDVAVRNN
VIIVMCDLCIRYTIMVDKYIPNISMCLKDSDPFIRKQTLILLTNLLQEEFVKWKGSLFFR
FVSTLIDSHPDIASFGEFCLAHLLLKRNPVMFFQHFIECIFHFNNYEKHEKYNKFPQSER
EKRLFSLKGKSNKERRMKIYKFLLEHFTDEQRFNITSKICLSILACFADGILPLDLDASE
LLSDTFEVLSSKEIKLLAMRSKPDKDLLMEEDDMALANVVMQEAQKKLISQVQKRNFIEN
IIPIIISLKTVLEKNKIPALRELMHYLREVMQDYRDELKDFFAVDKQLASELEYDMKKYQ
EQLVQEQELAKHADVAGTAGGAEVAPVAQVALCLETVPVPAGQENPAMSPAVSQPCTPRA
SAGHVAVSSPTPETGPLQRLLPKARPMSLSTIAILNSVKKAVESKSRHRSRSLGVLPFTL
NSGSPEKTCSQVSSYSLEQESNGEIEHVTKRAISTPEKSISDVTFGAGVSYIGTPRTPSS
AKEKIEGRSQGNDILCLSLPDKPPPQPQQWNVRSPARNKDTPACSRRSLRKTPLKTAN

Sequence length

1498

Interactions

View interactions

	Reactome
			Condensation of Prophase Chromosomes

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Microcephaly 22, primary, autosomal recessive	Pathogenic; Likely pathogenic	rs773824610, rs1164631127, rs2497410235, rs1555139372, rs1555143325, rs1350194762	RCV001334828 RCV003989183 RCV003990917 RCV000627672 RCV000627673 RCV000627674 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Adrenocortical carcinoma, hereditary	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE PRIMARY MICROCEPHALY	—	CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRONCHIECTASIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Benign; Conflicting classifications of pathogenicity; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NCAPD3-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (22)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Autosomal Recessive Primary Microcephaly	Microcephaly	ORPHANET_DG	27737959		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive primary microcephaly	Microcephaly	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	37457713	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	25701737	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	31885422	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	18223322		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MICROCEPHALY 22, PRIMARY, AUTOSOMAL RECESSIVE	Microcephaly	UNIPROT_DG	27737959		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MICROCEPHALY 22, PRIMARY, AUTOSOMAL RECESSIVE	Microcephaly	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neoplasms	Neoplasms	BEFREE	18223322		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuronal heterotopia	Neuronal Heterotopia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Oligospermia	Oligospermia	BEFREE	27692602		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	18223322		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	BEFREE	18223322		★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	BEFREE	25701737		★★★★★ ★☆☆☆☆ Found in Text Mining only
Unilateral agenesis of kidney	Renal aplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Vesico-Ureteral Reflux	Vesicoureteral Reflux	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

NCAPD3 (non-SMC condensin II complex subunit D3)