NCAPH2
protein-codingnon-SMC condensin II complex subunit H2, the group of Condensin II subunits
Gene summary
This gene encodes one of the non-SMC subunits of the condensin II complex. This complex plays an essential role in mitotic chromosome assembly. Alternate splicing of this gene results in multiple transcript variants.[provided by RefSeq, May 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NCAPH2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152299.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | 4 | ||
| missense | 108 | 6 | 1 | 115 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 11 | 11 | ||||
| Total | 0 | 0 | 120 | 7 | 3 | 130 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689512.2 | 20 | MANE Select | |
| Ensembl | ENSP00000410088.2 | 20 | MANE Select | |
| RefSeq | NP_001171940.1 | 20 | Standard | |
| RefSeq | NP_055366.3 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Condensation of Prophase Chromosomes
- Mitotic Prophase
- M Phase
- Cell Cycle
- Cell Cycle, Mitotic
Biological Process
- meiotic chromosome condensation
- T cell differentiation in thymus
- chromosome organization
- mitotic sister chromatid separation
- female meiosis chromosome separation
Molecular Function
- chromatin binding
- protein binding
Cellular Component
- condensed chromosome
- condensin complex
- nucleus
- nucleoplasm
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000299821
- Coding exons
- 20
- Length
- 15257
- Individuals with no LoFs
- 125716
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 32
- Defined
- 125748
- p
- 0.000127
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.176 | 346 | 355 | 0.974 | 0.0000214 | 3945 |
| Missense (PolyPhen) | 101 | 124.3 | 0.81255 | 1510 | ||
| Synonymous | -2.66 | 189 | 148 | 1.28 | 0.00000964 | 1159 |
| Loss of Function | 3.66 | 13 | 37.1 | 0.351 | 0.00000175 | 415 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00024 | 0.00023 | rare |
| European (Non-Finnish) | 0.00018 | 0.00017 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulatory subunit of the condensin-2 complex, a complex that seems to provide chromosomes with an additional level of organization and rigidity and in establishing mitotic chromosome architecture. May play a role in lineage-specific role in T-cell development (By similarity). {ECO:0000250, ECO:0000269|PubMed:14532007}.;
Recessive Scores
- pRec
- 0.0969
Intolerance Scores
- LoFtool
- 0.0236
- RVIS EVS
- -0.22
- RVIS percentile EVS
- 37.66
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.631
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |