NCAPH2

Chr 22

non-SMC condensin II complex subunit H2

Also known as: CAPH2

NCBI Gene: 29781ENSG00000025770UniProt: Q6IBW4OMIM: 611230

The NCAPH2 protein is a regulatory subunit of the condensin-2 complex that ensures proper mitotic chromosome condensation and organization, particularly critical during neurogenesis for accurate cell division in neural stem cells. Mutations cause microcephaly and developmental delay with autosomal recessive inheritance. This gene is highly intolerant to loss-of-function variants, reflecting its essential role in neurodevelopment.

OMIMResearchSummary from RefSeq, UniProt
LOEUF 0.56
Clinical Summary— NCAPH2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
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
0.18Z-score
OE missense 0.97 (0.89–1.06)
346 obs / 355.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.35 (0.23–0.56)
0≤0.351.4
Missense OE0.97 (0.89–1.06)
0≤0.61.4
Synonymous OE1.28
0≤1.21.6
LoF obs/exp: 13 / 37.1Missense obs/exp: 346 / 355.3Syn Z: -2.66

ClinVar Variant Classifications

0 submitted variants in ClinVar

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.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Associations Between Levels of Peripheral NCAPH2 Promoter Methylation and Different Stages of Alzheimer's Disease: A Cross-Sectional Study.
Hao SW et al.·J Alzheimers Dis
2023
Blood NCAPH2 Methylation Is Associated With Hippocampal Volume in Subjective Cognitive Decline With Apolipoprotein E ε4 Non-carriers.
Chen Y et al.·Front Aging Neurosci
2021Open Access
A commercial antibody to the human condensin II subunit NCAPH2 cross-reacts with a SWI/SNF complex component.
Cutts EE et al.·Wellcome Open Res
2021Open Access
Condensin II subunit NCAPH2 associates with shelterin protein TRF1 and is required for telomere stability.
Wallace HA et al.·J Cell Physiol
2019Open Access
DNA methylation in the NCAPH2/LMF2 promoter region is associated with hippocampal atrophy in Alzheimer's disease and amnesic mild cognitive impairment patients.
Shinagawa S et al.·Neurosci Lett
2016Cohort
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients