CPLANE1 p.Pro3046=
c.9138C>G · rs16903511 · VCV158059
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 9 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.11%, amr)
Conditions
2
Joubert syndrome 17
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.65 | GERP -0.36 |
| Overall | ||
| CADD | 0.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.11%
Admixed American · 2,465/60,006 alleles
Filtering AF
3.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.92%
Overall
0.225%
3,625/1,614,124 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 4.11% | 24 |
| East Asian | 2.02% | 50 |
| Remaining individualsnot grpmax-eligible | 0.208% | 481 |
| South Asian | 0.0791% | 1,265 |
| African / African-American | 0.0453% | 2,207 |
| European (non-Finnish) | 0.00161% | 62,105 |
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.Pro3046=
- Coding
- c.9138C>G
- MANE Select
- NM_001384732
- dbSNP
- rs16903511
- Type
- single nucleotide variant
- Location
- chr5:37121664 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 3046
- a UniProt-annotated variant site (in ofd6; likely pathogenic)
Similar variants
- 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
- CPLANE1 c.677+1G>C 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-pro3046 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown