PCNT

Chr 21AR

pericentrin

Also known as: KEN, MOPD2, PCN, PCNT2, PCNTB, PCTN2, SCKL4

NCBI Gene: 5116ENSG00000160299UniProt: O95613

The protein encoded by this gene binds to calmodulin and is expressed in the centrosome. It is an integral component of the pericentriolar material (PCM). The protein contains a series of coiled-coil domains and a highly conserved PCM targeting motif called the PACT domain near its C-terminus. The protein interacts with the microtubule nucleation component gamma-tubulin and is likely important to normal functioning of the centrosomes, cytoskeleton, and cell-cycle progression. Mutations in this gene cause Seckel syndrome-4 and microcephalic osteodysplastic primordial dwarfism type II. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

Primary Disease Associations & Inheritance

Microcephalic osteodysplastic primordial dwarfism, type IIMIM #210720
AR
4244
ClinVar variants
0
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— PCNT
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
4244 total variants — no pathogenic classifications of 4244 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
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.
0.82LOEUF
pLI 0.000
Z-score 3.53
OE 0.70 (0.61–0.82)
Tolerant

Typical tolerance to LoF variation

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.
-1.73Z-score
OE missense 1.11 (1.07–1.15)
2093 obs / 1881.5 exp
Tolerant

Tolerant to missense variation

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.0.70 (0.61–0.82)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.11 (1.07–1.15)
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.1.20
0≤1.21.6
LoF obs/exp: 117 / 166.1Missense obs/exp: 2093 / 1881.5Syn Z: -4.52

ClinVar Variant Classifications

4244 submitted variants in ClinVar

ClinVar

Classification Summary

Protein Context — Lollipop Plot

PCNT · protein map & ClinVar variants

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

Gene2Phenotype Curations

PCNT-related microcephalic osteodysplastic primordial dwarfism

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. DisordersSkeletal
G2P ↗

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
PERICENTRIN; PCNT
MIM #605925 · *

Microcephalic osteodysplastic primordial dwarfism, type II

MIM #210720

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
PCNT point mutations and familial intracranial aneurysms.
Lorenzo-Betancor O et al.·Neurology
2018
Hsa_circ_PCNT sponges hsa-miR-133b to promote SHH medulloblastoma via TAGLN2.
Wang Y et al.·Cell Mol Life Sci
2026
New PCNT candidate missense variant in a patient with oral and maxillofacial osteodysplasia: a case report.
Aoyama KI et al.·BMC Med Genet
2019Case report
The E3 ligase Poe promotes Pericentrin degradation.
Galletta BJ et al.·Mol Biol Cell
2023
Novel PCNT variants in MOPDII with attenuated growth restriction and pachygyria.
Waich S et al.·Clin Genet
2020
RAB33B and PCNT variants in two Pakistani families with skeletal dysplasia and short stature.
Ain NU et al.·BMC Musculoskelet Disord
2021
Modifier Genes in Microcephaly: A Report on WDR62, CEP63, RAD50 and PCNT Variants Exacerbating Disease Caused by Biallelic Mutations of ASPM and CENPJ.
Makhdoom EUH et al.·Genes (Basel)
2021Case report
Novel frameshift variant in the PCNT gene associated with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II and small kidneys.
Hettiarachchi D et al.·BMC Med Genomics
2022Case report
Genetic Findings in Short Turkish Children Born to Consanguineous Parents.
Joustra SD et al.·Horm Res Paediatr
2025
Antepartum nephrolithiasis and the risk of preterm delivery.
Drescher M et al.·Urolithiasis
2019
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Two Siblings With Microcephalic Osteodysplastic Primordial Dwarfism Type II (MOPDII) Caused by Compound Heterozygous Pericentrin (PCNT) Gene Variants.
Al Farsi A et al.·Cureus
2025🔓 Open Access
Hijacking a cellular highway: non-lipidated LC3 proteins and PCNT (pericentrin) drive influenza a virus uncoating.
Cong Y et al.·Autophagy
2026🔓 Open Access
PCNT is a prognostic biomarker correlated with tumor immune microenvironment in hepatocellular carcinoma and promotes tumor progression by inhibiting cell cycle arrest.
Wang X et al.·Aging (Albany NY)
2023🔓 Open Access
Case Report: short stature, kidney anomalies, and cerebral aneurysms in a novel homozygous mutation in the PCNT gene associated with microcephalic osteodysplastic primordial dwarfism type II.
Petraroli M et al.·Front Endocrinol (Lausanne)
2023🔓 Open AccessCase report
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