NCAPH2

Chr 22

non-SMC condensin II complex subunit H2

Also known as: CAPH2

NCBI Gene: 29781ENSG00000025770UniProt: Q6IBW4

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]

712
ClinVar variants
120
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NCAPH2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
120 Pathogenic / Likely Pathogenic· 211 VUS of 712 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.56LOEUF
pLI 0.000
Z-score 3.66
OE 0.35 (0.23–0.56)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.18Z-score
OE missense 0.97 (0.89–1.06)
346 obs / 355.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.35 (0.23–0.56)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.97 (0.89–1.06)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.28
0≤1.21.6
LoF obs/exp: 13 / 37.1Missense obs/exp: 346 / 355.3Syn Z: -2.66

ClinVar Variant Classifications

712 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic102
Likely Pathogenic18
VUS211
Likely Benign129
Benign4
Conflicting11
102
Pathogenic
18
Likely Pathogenic
211
VUS
129
Likely Benign
4
Benign
11
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
11
0
91
0
102
Likely Pathogenic
13
0
5
0
18
VUS
2
196
11
2
211
Likely Benign
0
8
2
119
129
Benign
0
1
2
1
4
Conflicting
—11
Total26205111122475

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

NCAPH2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Condensin II subunit NCAPH2 associates with shelterin protein TRF1 and is required for telomere stability.
Wallace HA et al.·J Cell Physiol
2019
Discovery and ranking of the most robust prognostic biomarkers in serous ovarian cancer.
Győrffy B·Geroscience
2023
Splice variants of the condensin II gene Ncaph2 include alternative reading frame translations of exon 1.
Theodoratos A et al.·FEBS J
2012
Recent Evidence in Epigenomics and Proteomics Biomarkers for Early and Minimally Invasive Diagnosis of Alzheimer's and Parkinson's Diseases.
Mayo S et al.·Curr Neuropharmacol
2021Review
Mutations in NCAPG2 Cause a Severe Neurodevelopmental Syndrome that Expands the Phenotypic Spectrum of Condensinopathies.
Khan TN et al.·Am J Hum Genet
2019
A novel role for the condensin II complex in cellular senescence.
Yokoyama Y et al.·Cell Cycle
2015
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools