CEP120

Chr 5AR

centrosomal protein 120

Also known as: CCDC100, JBTS31, SRTD13

NCBI Gene: 153241 ENSG00000168944 UniProt: Q8N960 OMIM: 613446

This gene encodes a protein that functions in the microtubule-dependent coupling of the nucleus and the centrosome. A similar protein in mouse plays a role in both interkinetic nuclear migration, which is a characteristic pattern of nuclear movement in neural progenitors, and in neural progenitor self-renewal. Mutations in this gene are predicted to result in neurogenic defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

GeneReviews OMIM Research

GeneReviews OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Joubert syndrome 31MIM #617761

Short-rib thoracic dysplasia 13 with or without polydactylyMIM #616300

Clinical highlights

Gene–disease validity (ClinGen)

Definitive · ciliopathy · AR · ClinGen 2025

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.80

LOEUF

LOF

Mechanism· G2P

📖

GeneReview available — CEP120

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.80LOEUF

pLI 0.000

Z-score 2.78

OE 0.59 (0.45–0.80)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.23Z-score

OE missense 1.03 (0.96–1.11)

525 obs / 510.2 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.59 (0.45–0.80)

0≤0.351.4

Missense OE?1.03 (0.96–1.11)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 32 / 54.1Missense obs/exp: 525 / 510.2Syn Z: -0.23

Background carrier burden — how many people carry a rare variant somewhere in CEP120?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 57

1,329 rare PASS variants

Rare truncating (LoF)

1 in 820

222 rare PASS variants

Rare synonymous (reference)

1 in 120

440 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CEP120. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 85	1 in 810
South Asian	~43k	1 in 35	1 in 600
Remaining (unassigned)	~30k	1 in 55	1 in 1,000
European (Finnish)	~27k	1 in 130	1 in 860
Admixed American	~22k	1 in 40	1 in 830
African / African American	~21k	1 in 35	1 in 830
East Asian	~20k	1 in 68	1 in 810
Ashkenazi Jewish	~13k	1 in 610	≈ 1 in 3,100
Middle Eastern	~2,884	1 in 41	≈ 1 in 950

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 15 of 20 coding exons well covered in gnomAD exomes; exons 10, 12, 14, 15, 18 marginal. Genomes: 19 of 20 (exon 10 below).? see exons ↓