CERT1 p.Ser2=
c.6G>A · rs138699646 · VCV791532
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.095%, amr)
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 5.6 | GERP 0.9, phastCons 1 |
| Overall | ||
| CADD | 16.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.095%
Admixed American · 57/59,990 alleles
Filtering AF
0.0752%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0681%
Overall
0.0133%
214/1,613,076 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.095% | 1,052 |
| Middle Eastern | 0.0495% | 2,020 |
| South Asian | 0.0362% | 2,760 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,679 |
| European (non-Finnish) | 0.00915% | 10,925 |
| African / African-American | 0.00267% | 37,520 |
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.Ser2=
- Coding
- c.6G>A
- MANE Select
- NM_001379029
- dbSNP
- rs138699646
- Type
- single nucleotide variant
- Location
- chr5:75511202 (GRCh38)
- Gene constraint
- LOEUF 0.656 · pLI 0.10 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.75 · 27 PDB
- Residue 2
- the 'disordered' region
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-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown