Is CPLANE1 p.Val413Ile (c.1237G>A) pathogenic?

CPLANE1 p.Val413Ile (c.1237G>A) is classified Uncertain significance in CPLANE1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-03). AlphaMissense: likely benign (0.0607); Very rare (popmax 0.00952%, sas); Associated with Joubert syndrome 17.

What condition is associated with CPLANE1 p.Val413Ile (c.1237G>A)?

CPLANE1 p.Val413Ile (c.1237G>A) is associated with Joubert syndrome 17, orofaciodigital syndrome type 6 (ClinVar).

How common is CPLANE1 p.Val413Ile (c.1237G>A) in the general population?

CPLANE1 p.Val413Ile (c.1237G>A) is very rare (popmax 0.00952%, sas) (gnomAD).

What do computational predictors say about CPLANE1 p.Val413Ile (c.1237G>A)?

AlphaMissense predicts likely benign (score 0.0607) — an in-silico prediction, not a clinical call.

CPLANE1 p.Val413Ile

c.1237G>A · rs758642292 · VCV1959847

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0607 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00952%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Joubert syndrome 17

Computational evidence

Protein change
AlphaMissense	0.0607	likely benign
REVEL	0.077	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 -0.6	GERP -3.2, phastCons 0.001
Regional constraint	o/e 0.92	unconstrained · MANE · 139 kb · p 2.3e-06 · regional, not allelic
Overall
CADD	6.582	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 0.00952% South Asian · 8/84,052 alleles

Filtering AF 0.00468% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00429%

Overall 0.00529% 82/1,551,210 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00952%	10,506
Remaining individualsnot grpmax-eligible	0.00666%	15,022
European (non-Finnish)	0.00584%	17,117
African / African-American	0.00274%	36,485
East Asian	0.00245%	40,878

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.Val413Ile
Coding: c.1237G>A
MANE Select: NM_001384732
dbSNP: rs758642292
Type: single nucleotide variant
Location: chr5:37227702 (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.Val413= Likely benign ★ 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-val413ile (accessed [today's date]).

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