CEP97

Chr 3

centrosomal protein 97

Also known as: 2810403B08Rik, LRRIQ2

NCBI Gene: 79598 ENSG00000182504 UniProt: Q8IW35 OMIM: 615864

Predicted to enable U2 snRNA binding activity and calmodulin binding activity. Involved in negative regulation of cilium assembly and regulation of mitotic spindle assembly. Located in centriole and centrosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

MultiplemechanismLOEUF 0.81

Clinical Summary— CEP97

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Population Constraint (gnomAD)

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

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 236 VUS of 360 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?

0.81LOEUF

pLI 0.000

Z-score 2.53

OE 0.58 (0.42–0.81)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.68Z-score

OE missense 0.91 (0.84–0.99)

410 obs / 450.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.58 (0.42–0.81)

0≤0.351.4

Missense OE?0.91 (0.84–0.99)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 24 / 41.6Missense obs/exp: 410 / 450.7Syn Z: 0.76

This gene — mechanism propensity

0.6745th %ile

GOF

0.6735th %ile

LOF

0.3355th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median

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

360 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Pathogenic1

VUS236

Likely Benign98

Benign12

Conflicting4

Likely Pathogenic

236

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	1	0	0	1
VUS	15	212	7	2	236
Likely Benign	0	11	26	61	98
Benign	0	3	2	7	12
Conflicting	—				4
Total	15	227	35	70	351

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

View in ClinVar →

10 pathogenic / likely-pathogenic (of 17) ClinVar copy-number / structural variants overlap CEP97 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →