CERT1 p.Pro9Leu
c.26C>T · rs768787922 · VCV3143203
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00821%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.027 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP 0.31, phastCons 0.94 |
| Overall | ||
| CADD | 13.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00821%
African / African-American · 6/73,068 alleles
Filtering AF
0.00354%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00243%
Overall
0.000645%
10/1,551,274 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00821% | 12,178 |
| Remaining individualsnot grpmax-eligible | 0.00333% | 30,041 |
| South Asian | 0.00119% | 84,022 |
| European (non-Finnish) | 8.72e-05% | 1,146,868 |
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
- CERT1
- Protein
- p.Pro9Leu
- Coding
- c.26C>T
- MANE Select
- NM_001379029 · reported on NM_001130105
- dbSNP
- rs768787922
- Type
- single nucleotide variant
- Location
- chr5:75511819 (GRCh38)
- Gene constraint
- LOEUF 0.656 · pLI 0.10 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.75 · 27 PDB
- Residue 9
- the 'disordered' region
Similar variants
- CERT1 p.Ser135Phe Likely pathogenic ★★ same condition
- CERT1 c.-195C>T Uncertain significance ★★ same condition
- CERT1 p.Ala538Val Uncertain significance ★★ ⚠ same condition
- CERT1 p.Cys185Phe Uncertain significance ★★ ⚠ same condition
- CERT1 p.Gly452Asp Uncertain significance ★★ ⚠ same condition
- CERT1 p.Met133Val Uncertain significance ★★ ⚠ same condition
- CERT1 c.-140C>T Likely benign ★★ same condition
- CERT1 p.Ile489Val Likely benign ★★ 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/cert1-p-pro9leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown