CPLANE1 p.Arg764=
c.2290A>C · rs1580891168 · VCV1444766
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000266%, nfe)
Conditions
2
orofaciodigital syndrome type 6
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 |
|---|---|---|
| Pangolin | Δ0.47 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 18.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000266%
European (non-Finnish) · 3/1,126,676 alleles
Filtering AF
7.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2e-05%
Overall
0.0002%
3/1,497,136 alleles · very rare
exomes 3/1,344,822 · genomes 0/152,314 · joint denominator
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.Arg764=
- Coding
- c.2290A>C
- MANE Select
- NM_001384732
- dbSNP
- rs1580891168
- Type
- single nucleotide variant
- Location
- chr5:37226305 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- CPLANE1 p.Arg764Lys 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-arg764 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown