CERS3 p.Thr357=
c.1071C>G · VCV4754140
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.185%, 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 0.15 | GERP 1.8 |
| Overall | ||
| CADD | 2.432 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.185%
South Asian · 168/91,052 alleles
Filtering AF
0.162%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.153%
Overall
0.011%
177/1,614,020 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.185% | 542 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,812 |
| European (non-Finnish) | 8.47e-05% | 1,179,960 |
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
- CERS3
- Protein
- p.Thr357=
- Coding
- c.1071C>G
- MANE Select
- NM_001378789
- Type
- single nucleotide variant
- Location
- chr15:100402794 (GRCh38)
- Gene constraint
- LOEUF 1.14 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.52
- Residue 357
- the 'disordered' region
Similar variants
- CERS3 c.466-1G>T Likely pathogenic ★★ same type
- CERS3 p.Arg75Ter Likely pathogenic ★★ same type
- CERS3 p.Arg275Cys Uncertain significance ★★ ⚠ same type
- CERS3 p.Ser177Phe Uncertain significance ★★ ⚠ same type
- CERS3 c.174-81G>A Benign ★★ same type
- CERS3 c.407+74C>T Benign ★★ same type
- CERS3 c.465+65A>T Benign ★★ same type
- CERS3 c.466-110G>T Benign ★★ 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/cers3-p-thr357 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown