CPLANE1 p.Ser337Pro
c.1009T>C · VCV4970084
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9375 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, REVEL · SaProt no call
Conditions
1
C5ORF42 & CPLANE1-related disorders
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9375 | likely pathogenic ✓ concordant with ClinVar · top 2% in CPLANE1 |
|---|---|---|
| REVEL | 0.272 | benign-leaning |
| SaProt | — | not scored · why |
| ⇒ AlphaMissense calls this damaging; REVEL does not; SaProt makes no call. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 0.92 | unconstrained · MANE · 139 kb · p 2.3e-06 · regional, not allelic |
| Overall | ||
| CADD | 25.5 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CPLANE1
- Protein
- p.Ser337Pro
- Coding
- c.1009T>C
- MANE Select
- NM_001384732
- Type
- single nucleotide variant
- Location
- chr5:37230979 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Disease context
C5ORF42 & CPLANE1-related disorders
Similar variants
- CPLANE1 p.Ser337Cys Uncertain significance ★ ⚠ same residue
- CPLANE1 c.1372-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CPLANE1 c.2920+1G>A Likely pathogenic ★★ same condition
- CPLANE1 c.7400+1G>A Pathogenic ★★ same condition
- CPLANE1 p.Ala1200Val Pathogenic ★★ same condition
- CPLANE1 p.Arg1226Ter Pathogenic/Likely pathogenic ★★ same condition
- CPLANE1 p.Arg2493Ter Pathogenic ★★ same condition
- CPLANE1 p.Arg2714Ter 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-ser337pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown