CLPB p.Ile318=
c.954T>C · rs1042741470 · VCV732296
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000205%)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.314 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.37 | GERP -2.4, phastCons 0.001 |
| Overall | ||
| CADD | 8.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000205%
Overall
0.000205%
3/1,459,972 alleles · very rare
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
- CLPB
- Protein
- p.Ile318=
- Coding
- c.954T>C
- MANE Select
- NM_001258392
- dbSNP
- rs1042741470
- Type
- single nucleotide variant
- Location
- chr11:72317140 (GRCh38)
- Gene constraint
- LOEUF 0.643 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.52 · 7 PDB
- Residue 318
- an α-helix
Similar variants
- CLPB c.1066+1G>A Pathogenic/Likely pathogenic ★★ same type
- CLPB c.455+1G>A Likely pathogenic ★★ same type
- CLPB c.873+1G>A Pathogenic/Likely pathogenic ★★ same type
- CLPB c.874-2A>G Likely pathogenic ★★ same type
- CLPB p.Arg178Ter Pathogenic ★★ same type
- CLPB p.Arg277Ter Pathogenic/Likely pathogenic ★★ same type
- CLPB p.Arg312Ter Pathogenic/Likely pathogenic ★★ same type
- CLPB p.Arg378Gly 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/clpb-p-ile318 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown