CEP162

Chr 6

centrosomal protein 162

Also known as: C6orf84, KIAA1009, QN1

NCBI Gene: 22832ENSG00000135315UniProt: Q5TB80

The protein is required for assembly of the transition zone in primary cilia by recognizing and binding axonemal microtubules and mediating CEP290 association with microtubules. Mutations cause Joubert syndrome and nephronophthisis, ciliopathies affecting the brain, kidneys, and other organ systems. The gene follows autosomal recessive inheritance.

ResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 0.98
Clinical Summary— CEP162
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
12 unique Pathogenic / Likely Pathogenic· 203 VUS of 259 total submissions
Explore recent and relevant literature in Research Assistant →
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.98LOEUF
pLI 0.000
Z-score 1.70
OE 0.77 (0.61–0.98)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.24Z-score
OE missense 1.03 (0.96–1.10)
646 obs / 628.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.77 (0.61–0.98)
0≤0.351.4
Missense OE1.03 (0.96–1.10)
0≤0.61.4
Synonymous OE1.00
0≤1.21.6
LoF obs/exp: 50 / 64.8Missense obs/exp: 646 / 628.8Syn Z: 0.04
DN
0.6840th %ile
GOF
0.5857th %ile
LOF
0.3259th %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

259 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic12
VUS203
Likely Benign15
Benign1
Conflicting3
12
Pathogenic
203
VUS
15
Likely Benign
1
Benign
3
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
12
0
12
Likely Pathogenic
0
0
0
0
0
VUS
0
186
17
0
203
Likely Benign
0
14
0
1
15
Benign
0
0
0
1
1
Conflicting
—3
Total0200292234

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

View in ClinVar →

Protein Context — Lollipop Plot

CEP162 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
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 3 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