CEP104

Chr 1AR

centrosomal protein 104

Also known as: CFAP256, GlyBP, JBTS25, KIAA0562, MRT77, ROC22

This gene encodes a centrosomal protein required for ciliogenesis and for ciliary tip structural integrity. The mammalian protein contains three amino-terminal hydrophobic domains, two glycosylation sites, four cysteine-rich motifs, and two regions with homology to the glutamate receptor ionotropic, NMDA 1 protein. During ciliogenesis, the encoded protein translocates from the distal tips of the centrioles to the tip of the elongating cilium. Knockdown of the protein in human retinal pigment cells results in severe defects in ciliogenesis with structural deformities at the ciliary tips. Allelic variants of this gene are associated with the autosomal-recessive disorder Joubert syndrome, which is characterized by a distinctive mid-hindbrain and cerebellar malformation, oculomotor apraxia, irregular breathing, developmental delay, and ataxia. [provided by RefSeq, Feb 2016]

Primary Disease Associations & Inheritance

Intellectual developmental disorder, autosomal recessive 77MIM #619988
AR
Joubert syndrome 25MIM #616781
AR
0
Active trials
84
Pathogenic / LP
477
ClinVar variants
3
Pubs (1 yr)
0.4
Missense Z
0.74
LOEUF
Clinical SummaryCEP104
🧬
Gene-Disease Validity (ClinGen)
ciliopathy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
84 Pathogenic / Likely Pathogenic· 194 VUS of 477 total submissions
📖
GeneReview available — CEP104
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.74LOEUF
pLI 0.000
Z-score 3.05
OE 0.54 (0.400.74)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.44Z-score
OE missense 0.95 (0.881.02)
503 obs / 531.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.54 (0.400.74)
00.351.4
Missense OE0.95 (0.881.02)
00.61.4
Synonymous OE0.85
01.21.6
LoF obs/exp: 28 / 51.7Missense obs/exp: 503 / 531.8Syn Z: 1.65

ClinVar Variant Classifications

477 submitted variants in ClinVar

Classification Summary

Pathogenic53
Likely Pathogenic31
VUS194
Likely Benign164
Benign18
Conflicting17
53
Pathogenic
31
Likely Pathogenic
194
VUS
164
Likely Benign
18
Benign
17
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
10
0
43
0
53
Likely Pathogenic
18
0
13
0
31
VUS
1
178
14
1
194
Likely Benign
0
16
65
83
164
Benign
2
3
9
4
18
Conflicting
17
Total3119714488477

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

View in ClinVar →

CEP104 · protein map & ClinVar variants

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

Gene2Phenotype Curations

CEP104-related Joubert syndrome

definitive
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

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence