CPLANE1 p.Arg1184His
c.3551G>A · rs548645125 · VCV2734718
Computational evidence
| Protein change | ||
| AlphaMissense | 0.7501 | likely pathogenic · top 7% in CPLANE1 |
|---|---|---|
| REVEL | 0.797 | moderately pathogenic-leaning |
| ⇒ AlphaMissense and REVEL both call this damaging. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.6, phastCons 1 |
| Regional constraint | o/e 0.92 | unconstrained · MANE · 139 kb · p 2.3e-06 · regional, not allelic |
| Overall | ||
| CADD | 28.8 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,496 |
| European (non-Finnish)grpmax | 0.00144% | 69,403 |
| South Asian | 0.0011% | 91,068 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Arg1184His
- Coding
- c.3551G>A
- MANE Select
- NM_001384732
- dbSNP
- rs548645125
- Type
- single nucleotide variant
- Location
- chr5:37198823 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1184
- a UniProt-annotated variant site (in ofd6); a UniProt-annotated variant site (in ofd6; likely pathogenic)
Similar variants
- CPLANE1 p.Arg1184Cys Conflicting classifications of pathogenicity ★ same residue
- 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
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-arg1184his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown