Is CPLANE1 p.Val1366Met (c.4096G>A) pathogenic?

CPLANE1 p.Val1366Met (c.4096G>A) is classified Conflicting classifications of pathogenicity in CPLANE1 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-11-18). AlphaMissense: likely benign (0.2724); Ultra-rare (popmax 0.0426%, eas); Associated with Joubert syndrome 17.

What condition is associated with CPLANE1 p.Val1366Met (c.4096G>A)?

CPLANE1 p.Val1366Met (c.4096G>A) is associated with Joubert syndrome 17, orofaciodigital syndrome type 6 (ClinVar).

How common is CPLANE1 p.Val1366Met (c.4096G>A) in the general population?

CPLANE1 p.Val1366Met (c.4096G>A) is ultra-rare (popmax 0.0426%, eas) (gnomAD).

What do computational predictors say about CPLANE1 p.Val1366Met (c.4096G>A)?

AlphaMissense predicts likely benign (score 0.2724) — an in-silico prediction, not a clinical call.

CPLANE1 p.Val1366Met

c.4096G>A · rs781367784 · VCV1587210

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2724 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0426%, eas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Joubert syndrome 17

Computational evidence

Protein change
AlphaMissense	0.2724	likely benign
REVEL	0.064	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -0.28, phastCons 0.97
Regional constraint	o/e 0.92	unconstrained · MANE · 139 kb · p 2.3e-06 · regional, not allelic
Overall
CADD	20.9	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0426% East Asian · 19/44,648 alleles

Filtering AF 0.0278% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0231%

Overall 0.00329% 52/1,582,462 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0426%	2,350
Remaining individualsnot grpmax-eligible	0.00489%	20,457
European (non-Finnish)	0.00234%	42,769
Admixed American	0.00169%	59,068
African / African-American	0.00134%	74,400
South Asian	0.00113%	88,280

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: CPLANE1
Protein: p.Val1366Met
Coding: c.4096G>A
MANE Select: NM_001384732
dbSNP: rs781367784
Type: single nucleotide variant
Location: chr5:37186379 (GRCh38)
Gene constraint: LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

Full CPLANE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome 17 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: orofaciodigital syndrome type 6

Similar variants

CPLANE1 p.Val1366Leu Uncertain significance ★ ⚠ same residue
CPLANE1 c.1372-2A>G Pathogenic/Likely pathogenic ★★ same condition
CPLANE1 c.2291+1G>A Likely pathogenic ★★ same condition
CPLANE1 c.2291+2T>C Pathogenic/Likely pathogenic ★★ same condition
CPLANE1 c.2292-1G>A Likely pathogenic ★★ same condition
CPLANE1 c.2500+1G>A Likely pathogenic ★★ same condition
CPLANE1 c.3290-2A>G Pathogenic/Likely pathogenic ★★ same condition
CPLANE1 c.3673-1G>C Pathogenic/Likely pathogenic ★★ 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/cplane1-p-val1366met (accessed [today's date]).

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