Is CEP41 p.Pro324Leu (c.971C>T) pathogenic?

CEP41 p.Pro324Leu (c.971C>T) is classified Uncertain significance in CEP41 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-07-17). AlphaMissense: likely benign (0.0717); Ultra-rare (popmax 0.0216%, mid); Associated with Joubert syndrome 15.

What condition is associated with CEP41 p.Pro324Leu (c.971C>T)?

CEP41 p.Pro324Leu (c.971C>T) is associated with Joubert syndrome 15 (ClinVar).

How common is CEP41 p.Pro324Leu (c.971C>T) in the general population?

CEP41 p.Pro324Leu (c.971C>T) is ultra-rare (popmax 0.0216%, mid) (gnomAD).

What do computational predictors say about CEP41 p.Pro324Leu (c.971C>T)?

AlphaMissense predicts likely benign (score 0.0717) — an in-silico prediction, not a clinical call.

CEP41 p.Pro324Leu

c.971C>T · rs782474335 · VCV1485026

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0717 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0216%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Joubert syndrome 15

Computational evidence

Protein change
AlphaMissense	0.0717	likely benign
REVEL	0.18	moderately benign-leaning
SaProt	LLR -6.56	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 5.6	GERP -0.46, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 42 kb · p 0.28 · regional, not allelic
Overall
CADD	22.4	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 0.0216% Middle Eastern · 1/4,630 alleles

Filtering AF 0.000251% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000161%

Overall 0.000755% 12/1,589,860 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0216%	4,630
Remaining individualsnot grpmax-eligible	0.00487%	20,535
South Asian	0.0011%	90,532
European (non-Finnish)	0.000604%	165,659

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: CEP41
Protein: p.Pro324Leu
Coding: c.971C>T
MANE Select: NM_018718
dbSNP: rs782474335
Type: single nucleotide variant
Location: chr7:130400041 (GRCh38)
Gene constraint: LOEUF 1.066 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.06 · 1 PDB
Residue 324: the 'disordered' region

Full CEP41 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome 15 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEP41 c.34-2A>G Pathogenic/Likely pathogenic ★★ same condition
CEP41 c.423-2A>C Pathogenic ★★ same condition
CEP41 p.Arg286Ter Pathogenic/Likely pathogenic ★★ same condition
CEP41 p.Gln140Ter Pathogenic ★★ same condition
CEP41 c.33+6G>A Uncertain significance ★★ same condition
CEP41 c.*2116T>C Uncertain significance ★★ same condition
CEP41 c.*2389G>A Uncertain significance ★★ same condition
CEP41 p.Ala103Val Uncertain significance ★★ ⚠ same condition

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/cep41-p-pro324leu (accessed [today's date]).

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