CPLANE1 p.Ile857=
c.2571C>T · rs749918295 · VCV2697205
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
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 -0.027 | GERP -1.3, phastCons 0.036 |
| Overall | ||
| CADD | 5.643 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,998 alleles
Filtering AF
0.00162%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000956%
Overall
0.00142%
22/1,546,354 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,998 |
| South Asian | 0.00481% | 20,809 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,926 |
| European (non-Finnish) | 0.0014% | 71,487 |
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.Ile857=
- Coding
- c.2571C>T
- MANE Select
- NM_001384732
- dbSNP
- rs749918295
- Type
- single nucleotide variant
- Location
- chr5:37224263 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- CPLANE1 c.1372-2A>G Pathogenic/Likely pathogenic ★★ same type
- CPLANE1 c.2291+1G>A Likely pathogenic ★★ same type
- CPLANE1 c.2291+2T>C Pathogenic/Likely pathogenic ★★ same type
- CPLANE1 c.2292-1G>A Likely pathogenic ★★ same type
- CPLANE1 c.2500+1G>A Likely pathogenic ★★ same type
- CPLANE1 c.2920+1G>A Likely pathogenic ★★ same type
- CPLANE1 c.3290-2A>G Pathogenic/Likely pathogenic ★★ same type
- CPLANE1 c.3673-1G>C Pathogenic/Likely pathogenic ★★ same type
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-ile857 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown