CERT1 p.Ala111=
c.333C>T · VCV4848029
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 2.4 | GERP -0.46, phastCons 1 |
| Overall | ||
| CADD | 11.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,792 alleles
Filtering AF
0.000185%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000122%
Overall
0.000438%
7/1,599,192 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,792 |
| European (non-Finnish) | 0.000514% | 194,462 |
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.Ala111=
- Coding
- c.333C>T
- MANE Select
- NM_001379029
- Type
- single nucleotide variant
- Location
- chr5:75459080 (GRCh38)
- Gene constraint
- LOEUF 0.656 · pLI 0.10 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.75 · 27 PDB
- Residue 111
- the ph domain; an α-helix
Similar variants
- CERT1 p.Ser135Phe Likely pathogenic ★★ same type
- CERT1 p.Thr166Ala Pathogenic/Likely pathogenic ★★ ⚠ same type
- CERT1 c.-195C>T Uncertain significance ★★ same type
- CERT1 p.Ala538Val Uncertain significance ★★ ⚠ same type
- CERT1 p.Asp80Asn Uncertain significance ★★ ⚠ same type
- CERT1 p.Cys185Phe Uncertain significance ★★ ⚠ same type
- CERT1 p.Gly452Asp Uncertain significance ★★ ⚠ same type
- CERT1 p.Lys48Asn Uncertain significance ★★ ⚠ 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/cert1-p-ala111 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown