Is CPLANE1 p.Pro2136fs (c.6407del) pathogenic?

CPLANE1 p.Pro2136fs (c.6407del) is classified Pathogenic in CPLANE1 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2012-04-06). Absent from gnomAD; Associated with Joubert syndrome 17.

What condition is associated with CPLANE1 p.Pro2136fs (c.6407del)?

CPLANE1 p.Pro2136fs (c.6407del) is associated with Joubert syndrome 17 (ClinVar).

How common is CPLANE1 p.Pro2136fs (c.6407del) in the general population?

CPLANE1 p.Pro2136fs (c.6407del) is absent from gnomAD (gnomAD).

CPLANE1 p.Pro2136fs

c.6407del · rs367543064 · VCV31221

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Joubert syndrome 17

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 33 of 53
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.8	GERP -2.4

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CPLANE1
Protein: p.Pro2136fs
Coding: c.6407del
MANE Select: NM_001384732
dbSNP: rs367543064
Type: Deletion
Location: chr5:37170096 (GRCh38)
Gene constraint: LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2136: the 'disordered' region

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

Similar variants

CPLANE1 p.Asn1182fs Pathogenic ★★ same condition
CPLANE1 p.Gly2717fs Pathogenic ★★ same condition
CPLANE1 p.Ile165fs Pathogenic ★★ same condition
CPLANE1 p.Ile1889_Asp1890insTer Likely pathogenic ★★ same condition
CPLANE1 p.Leu465fs Pathogenic/Likely pathogenic ★★ same condition
CPLANE1 p.Lys1071fs Likely pathogenic ★★ same condition
CPLANE1 p.Lys1186fs Pathogenic/Likely pathogenic ★★ same condition
CPLANE1 p.Lys2345fs 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-pro2136fs (accessed [today's date]).

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