Is CEP41 p.Cys240= (c.720C>T) pathogenic?

CEP41 p.Cys240= (c.720C>T) is classified Likely benign in CEP41 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-05-25). Ultra-rare (popmax 0.0143%, sas); Associated with Joubert syndrome 15.

What condition is associated with CEP41 p.Cys240= (c.720C>T)?

CEP41 p.Cys240= (c.720C>T) is associated with Joubert syndrome 15 (ClinVar).

How common is CEP41 p.Cys240= (c.720C>T) in the general population?

CEP41 p.Cys240= (c.720C>T) is ultra-rare (popmax 0.0143%, sas) (gnomAD).

CEP41 p.Cys240=

c.720C>T · rs556325841 · VCV2077915

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0143%, sas)

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 · G>T here scores Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP -6.2	GERP -5.2
Overall
CADD	1.286	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0143% South Asian · 13/90,874 alleles

Filtering AF 0.00846% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00663%

Overall 0.000992% 16/1,613,432 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0143%	6,990
Remaining individualsnot grpmax-eligible	0.0016%	62,486
European (non-Finnish)	0.00017%	589,793

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.Cys240=
Coding: c.720C>T
MANE Select: NM_018718
dbSNP: rs556325841
Type: single nucleotide variant
Location: chr7:130400744 (GRCh38)
Gene constraint: LOEUF 1.066 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.06 · 1 PDB
Residue 240: the rhodanese domain; a UniProt-annotated variant site (found in a patient with autism; uncertain significance)

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.Cys240Gly Benign/Likely benign ★★ ⚠ 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-cys240 (accessed [today's date]).

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