Is CEP41 p.Pro120= (c.360G>A) pathogenic?

CEP41 p.Pro120= (c.360G>A) is classified Likely benign in CEP41 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-04). Ultra-rare (popmax 0.0164%, mid); Associated with Joubert syndrome 15.

What condition is associated with CEP41 p.Pro120= (c.360G>A)?

CEP41 p.Pro120= (c.360G>A) is associated with Joubert syndrome 15 (ClinVar).

How common is CEP41 p.Pro120= (c.360G>A) in the general population?

CEP41 p.Pro120= (c.360G>A) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

CEP41 p.Pro120=

c.360G>A · rs148169407 · VCV2168627

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

Joubert syndrome 15

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP -1.6	GERP -4.8
Overall
CADD	6.36	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.000806% 13/1,613,488 alleles · ultra-rare exomes 11/1,461,332 · genomes 2/152,156 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
South Asian	0.00439%	22,770
African / African-American	0.00267%	37,448
Admixed American	0.00167%	60,006
European (non-Finnish)	0.000424%	235,906

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.Pro120=
Coding: c.360G>A
MANE Select: NM_018718
dbSNP: rs148169407
Type: single nucleotide variant
Location: chr7:130404626 (GRCh38)
Gene constraint: LOEUF 1.066 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.06 · 1 PDB
Residue 120: 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 p.Pro120Arg Uncertain significance ★ ⚠ same residue
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

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-pro120 (accessed [today's date]).

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