NCAPD2 non-SMC condensin I complex subunit D2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NCAPD2provided by HGNC
Official Full Name: non-SMC condensin I complex subunit D2provided by HGNC
Primary source: HGNC:HGNC:24305
See related: Ensembl:ENSG00000010292 MIM:615638; AllianceGenome:HGNC:24305
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CNAP1; CAP-D2; MCPH21; hCAP-D2
Summary: Enables histone binding activity. Involved in mitotic chromosome condensation and positive regulation of chromosome condensation. Located in condensed chromosome; cytosol; and nuclear lumen. Part of condensin complex. Implicated in primary autosomal recessive microcephaly. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in lymph node (RPKM 20.3), bone marrow (RPKM 14.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (6494102..6531955)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (6504453..6542311)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (6603268..6641121)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Non-SMC condensin I complex subunit D2 (NCAPD2) reveals its prognostic and immunologic features in human cancers.
Title: Non-SMC condensin I complex subunit D2 (NCAPD2) reveals its prognostic and immunologic features in human cancers.
NCAPD2 promotes breast cancer progression through E2F1 transcriptional regulation of CDK1.
Title: NCAPD2 promotes breast cancer progression through E2F1 transcriptional regulation of CDK1.
NCAPD2 is a novel marker for the poor prognosis of lung adenocarcinoma and is associated with immune infiltration and tumor mutational burden.
Title: NCAPD2 is a novel marker for the poor prognosis of lung adenocarcinoma and is associated with immune infiltration and tumor mutational burden.
NCAPD2 inhibits autophagy by regulating Ca(2+)/CAMKK2/AMPK/mTORC1 pathway and PARP-1/SIRT1 axis to promote colorectal cancer.
Title: NCAPD2 inhibits autophagy by regulating Ca(2+)/CAMKK2/AMPK/mTORC1 pathway and PARP-1/SIRT1 axis to promote colorectal cancer.
this is the second report of primary microcephaly due to a pathogenic variant at the NCAPD2 gene. We found two affected siblings who carried a splice-site pathogenic variant (c.3477+2T>C). Our finding provided accurate diagnosis and genetic counseling to the family.
Title: A novel homozygous splice-site variant of NCAPD2 gene identified in two siblings with primary microcephaly: The second case report.
NCAPD2 and NCAPD3 expression levels have been confirmed to be significantly up-regulated in the intestinal mucosa of patients with active ulcerative colitis. In vitro, the data suggested that silencing NACPD2 and NACPD3 could depress the expression of IL-1beta, IL-6 and TNF-alpha. Further, knockdown of NACPD2 and NACPD3 could remarkably suppress IKK nucleation and NF-kappaB volume.
Title: Non-SMC condensin I complex subunit D2 and non-SMC condensin II complex subunit D3 induces inflammation via the IKK/NF-κB pathway in ulcerative colitis.
High NCAPD2 expression was associated with lymph node metastasis in Triple-Negative Breast Cancer.
Title: Non-SMC Condensin I Complex Subunit D2 Is a Prognostic Factor in Triple-Negative Breast Cancer for the Ability to Promote Cell Cycle and Enhance Invasion.
The authors propose that histone H3 threonine 118 phosphorylation via Aurora-A alters the chromatin structure during specific phases of mitosis to promote timely condensin I and cohesin disassociation, which is essential for effective chromosome segregation.
Title: Aurora-A mediated histone H3 phosphorylation of threonine 118 controls condensin I and cohesin occupancy in mitosis.
Study has shown that both rs7311174 and rs2072374 in the NCAPD2 gene are associated with Parkinson's disease in a Han Chinese population.
Title: Non-SMC condensin I complex, subunit D2 gene polymorphisms are associated with Parkinson's disease: a Han Chinese study.
Data show that that DNA repear process is dictated by PARP1 through its interaction with the chromosome-targeting domain of the hCAP-D2 subunit of condensin I.
Title: Condensin I recruitment to base damage-enriched DNA lesions is modulated by PARP1.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Microcephaly 21, primary, autosomal recessive MedGen: C4693831 OMIM: 617983 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Interaction of HIV-1 Tat with CAPD2 in T-cells is identified by a proteomic strategy based on affinity chromatography coupled with mass spectrometry	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH93703 (e-PCR)
- UniSTS:87571

G41276 (e-PCR)
- UniSTS:54306

D11S2560 (e-PCR)
- UniSTS:37928

WI-21900 (e-PCR)
- UniSTS:11077

D12S229 (e-PCR)
- UniSTS:30312

D15S1477 (e-PCR)
- UniSTS:474482

RH25377 (e-PCR)
- UniSTS:88458

D12S924 (e-PCR)
- UniSTS:149924

RH48486 (e-PCR)
- UniSTS:68822

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in meiotic chromosome condensation	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic chromosome condensation	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic chromosome condensation	IDA Inferred from Direct Assay more info	PubMed
involved_in mitotic chromosome condensation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic chromosome condensation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of chromosome condensation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of chromosome segregation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of chromosome separation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in condensed chromosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in condensed chromosome, centromeric region	IBA Inferred from Biological aspect of Ancestor more info
located_in condensed nuclear chromosome	ISO Inferred from Sequence Orthology more info
part_of condensin complex	IBA Inferred from Biological aspect of Ancestor more info
part_of condensin complex	IDA Inferred from Direct Assay more info	PubMed
part_of condensin complex	NAS Non-traceable Author Statement more info	PubMed
colocalizes_with cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
colocalizes_with nuclear chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: condensin complex subunit 1

Names: XCAP-D2 homolog; chromosome condensation-related SMC-associated protein 1; chromosome-associated protein D2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_014865.4 → NP_055680.3 condensin complex subunit 1

See identical proteins and their annotated locations for NP_055680.3

Status: VALIDATED

Source sequence(s)

AC006064, AK022511, AK128354, AL548223, BC028182, CN307514, D63880

Consensus CDS

CCDS8548.1

UniProtKB/Swiss-Prot

D3DUR4, Q15021, Q8N6U3

UniProtKB/TrEMBL

B3KMS0

Related

ENSP00000325017.5, ENST00000315579.10

Conserved Domains (3) summary

COG5098
Location:60 → 1245

COG5098; Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics / Cell division and chromosome partitioning]

pfam12717
Location:1069 → 1234

Cnd1; non-SMC mitotic condensation complex subunit 1

pfam12922
Location:75 → 240

Cnd1_N; non-SMC mitotic condensation complex subunit 1, N-term