NCAPD3

Chr 11AR

non-SMC condensin II complex subunit D3

Also known as: CAP-D3, CAPD3, MCPH22, hCAP-D3, hHCP-6, hcp-6

NCBI Gene: 23310ENSG00000151503UniProt: P42695

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 sets of non-SMC subunits. NCAPD3 is 1 of 3 non-SMC subunits that define condensin II (Ono et al., 2003 [PubMed 14532007]).[supplied by OMIM, Mar 2008]

Primary Disease Associations & Inheritance

Microcephaly 22, primary, autosomal recessiveMIM #617984
AR
0
Active trials
98
Pathogenic / LP
452
ClinVar variants
7
Pubs (1 yr)
-0.7
Missense Z
0.49
LOEUF
Clinical Summary— NCAPD3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
98 Pathogenic / Likely Pathogenic· 273 VUS of 452 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.49LOEUF
pLI 0.000
Z-score 5.40
OE 0.36 (0.27–0.49)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
-0.73Z-score
OE missense 1.07 (1.01–1.13)
876 obs / 817.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.36 (0.27–0.49)
0≤0.351.4
Missense OE1.07 (1.01–1.13)
0≤0.61.4
Synonymous OE1.24
0≤1.21.6
LoF obs/exp: 30 / 83.1Missense obs/exp: 876 / 817.4Syn Z: -3.36

ClinVar Variant Classifications

452 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic87
Likely Pathogenic11
VUS273
Likely Benign58
Benign20
Conflicting3
87
Pathogenic
11
Likely Pathogenic
273
VUS
58
Likely Benign
20
Benign
3
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
1
83
0
87
Likely Pathogenic
2
0
9
0
11
VUS
2
255
16
0
273
Likely Benign
0
18
13
27
58
Benign
0
11
4
5
20
Conflicting
—3
Total728512532452

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

View in ClinVar →

NCAPD3 · protein map & ClinVar variants

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

Gene2Phenotype Curations

NCAPD3-related microcephaly with short stature

limited
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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