CEP83

Chr 12AR

centrosomal protein 83

Also known as: CCDC41, NPHP18, NY-REN-58

NCBI Gene: 51134 ENSG00000173588 UniProt: Q9Y592 OMIM: 615847

The encoded protein is a centriolar component that initiates primary cilium assembly and collaborates with IFT20 in trafficking ciliary membrane proteins from the Golgi complex to the cilium. Mutations cause nephronophthisis 18, an infantile kidney disorder that can be associated with intellectual disability. The condition follows autosomal recessive inheritance.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene is a centriolar protein involved in primary cilium assembly. Defects in this gene have been associated with infantile nephronophthisis and intellectual disability. [provided by RefSeq, Oct 2016]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.891 OMIM phenotype

Clinical Summary— CEP83

⚡

Population Constraint (gnomAD)

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

📋

ClinVar Variants

47 unique Pathogenic / Likely Pathogenic· 263 VUS of 607 total submissions

Explore recent and relevant literature in Research Assistant →

📖

GeneReview available — CEP83

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?

0.89LOEUF

pLI 0.000

Z-score 2.12

OE 0.65 (0.48–0.89)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.41Z-score

OE missense 0.94 (0.85–1.03)

316 obs / 337.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.65 (0.48–0.89)

0≤0.351.4

Missense OE?0.94 (0.85–1.03)

0≤0.61.4

Synonymous OE?1.11

0≤1.21.6

LoF obs/exp: 28 / 43.0Missense obs/exp: 316 / 337.0Syn Z: -0.95

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitiveCEP83-related infantile nephronophthisis and intellectual disabilityLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.76top 25%

GOF

0.6442th %ile

LOF

0.3261th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

607 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic37

Likely Pathogenic10

VUS263

Likely Benign223

Benign41

Conflicting13

Pathogenic

Likely Pathogenic

263

VUS

223

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	33	3	1	0	37
Likely Pathogenic	8	2	0	0	10
VUS	1	248	13	1	263
Likely Benign	0	10	93	120	223
Benign	0	3	33	5	41
Conflicting	—				13
Total	42	266	140	126	587

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

View in ClinVar →

6 pathogenic / likely-pathogenic (of 8) ClinVar copy-number / structural variants overlap CEP83 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →