CERT1 p.Ala245=
c.735G>A · rs200264269 · VCV788983
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.155%, sas)
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 -6.1 | GERP -5.6 |
| Overall | ||
| CADD | 4.023 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.155%
South Asian · 141/90,994 alleles
Filtering AF
0.134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.126%
Overall
0.0195%
314/1,611,862 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.155% | 645 |
| Ashkenazi Jewishnot grpmax-eligible | 0.149% | 672 |
| Remaining individualsnot grpmax-eligible | 0.0384% | 2,601 |
| Middle Eastern | 0.033% | 3,026 |
| Admixed American | 0.0317% | 3,158 |
| African / African-American | 0.00934% | 10,707 |
| European (non-Finnish) | 0.00645% | 15,501 |
| Finnishnot grpmax-eligible | 0.00156% | 64,020 |
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.Ala245=
- Coding
- c.735G>A
- MANE Select
- NM_001379029
- dbSNP
- rs200264269
- Type
- single nucleotide variant
- Location
- chr5:75416978 (GRCh38)
- Gene constraint
- LOEUF 0.656 · pLI 0.10 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.75 · 27 PDB
Similar variants
- CERT1 p.Ala245Val Uncertain significance ★ ⚠ same residue
- 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
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-ala245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown