Is CEP152 p.Cys56Arg (c.166T>C) pathogenic?

CEP152 p.Cys56Arg (c.166T>C) is classified Uncertain significance in CEP152 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-26). AlphaMissense: likely benign (0.241); Very rare (popmax 0.000678%, nfe).

How common is CEP152 p.Cys56Arg (c.166T>C) in the general population?

CEP152 p.Cys56Arg (c.166T>C) is very rare (popmax 0.000678%, nfe) (gnomAD).

What do computational predictors say about CEP152 p.Cys56Arg (c.166T>C)?

AlphaMissense predicts likely benign (score 0.241) — an in-silico prediction, not a clinical call.

CEP152 p.Cys56Arg

c.166T>C · VCV4771426

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.241 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000678%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.241	likely benign
REVEL	0.182	moderately benign-leaning
SaProt	LLR -6.19	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP 5.3, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 67 kb · p 0.21 · regional, not allelic
Overall
CADD	19.74	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000678% European (non-Finnish) · 8/1,179,978 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000547% 8/1,461,754 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CEP152
Protein: p.Cys56Arg
Coding: c.166T>C
MANE Select: NM_001194998
Type: single nucleotide variant
Location: chr15:48797973 (GRCh38)
Gene constraint: LOEUF 0.784 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.54 · 3 PDB
Residue 56: the 'interaction with plk4' region; the 'disordered' region

Full CEP152 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP152 p.Cys56Tyr Uncertain significance ★ ⚠ same residue
CEP152 c.1578-1G>A Likely pathogenic ★★ same type
CEP152 c.1908+1G>T Likely pathogenic ★★ same type
CEP152 c.540+1G>A Pathogenic/Likely pathogenic ★★ same type
CEP152 c.88-2A>G Likely pathogenic ★★ same type
CEP152 c.972+2T>A Likely pathogenic ★★ same type
CEP152 p.Arg115Ter Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Arg1309Ter Pathogenic/Likely pathogenic ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cep152-p-cys56arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown