CEP20

Chr 16

centrosomal protein 20

Also known as: C16orf63, FOPNL, FOR20, PHSECRG2

NCBI Gene: 123811 ENSG00000133393 UniProt: Q96NB1 OMIM: 617149

CEP20 encodes a protein that enables identical protein binding and is involved in cilium assembly and centrosome function, specifically recruiting PLK1 to centrosomes for S phase progression. Mutations cause Joubert syndrome, a ciliopathy characterized by cerebellar vermis hypoplasia, developmental delays, and other neurological features, following an autosomal recessive inheritance pattern. The gene shows low constraint against loss-of-function variants (pLI near 0, LOEUF 1.624), consistent with recessive disease mechanisms.

OMIM ResearchSummary from RefSeq, UniProt

Enables identical protein binding activity. Involved in cilium assembly. Located in centriolar satellite; ciliary basal body; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.62

Clinical Summary— CEP20

⚡

Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

📋

ClinVar Variants

27 VUS of 35 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.62LOEUF

pLI 0.000

Z-score 0.14

OE 0.95 (0.57–1.62)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.59Z-score

OE missense 1.18 (1.00–1.39)

103 obs / 87.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.95 (0.57–1.62)

0≤0.351.4

Missense OE?1.18 (1.00–1.39)

0≤0.61.4

Synonymous OE?0.92

0≤1.21.6

LoF obs/exp: 9 / 9.5Missense obs/exp: 103 / 87.5Syn Z: 0.35

This gene — mechanism propensity

0.6842th %ile

GOF

0.4875th %ile

LOF

0.3843th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

35 submitted variants in ClinVar

ClinVar

Classification Summary

VUS27

Likely Benign2

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	27	0	27
Likely Benign	1	1	2
Benign	0	0	0
Total	28	1	29

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

View in ClinVar →

220 pathogenic / likely-pathogenic (of 373) ClinVar copy-number / structural variants overlap CEP20 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →