CERS3 p.Thr109=
c.327G>A · rs115592596 · VCV774948
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.957%, afr)
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 -3.7 | GERP -4.2 |
| Overall | ||
| CADD | 5.986 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.957%
African / African-American · 718/75,014 alleles
Filtering AF
0.899%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.876%
Overall
0.051%
823/1,614,040 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.957% | 104 |
| Middle Eastern | 0.148% | 674 |
| Remaining individualsnot grpmax-eligible | 0.0896% | 1,116 |
| Admixed American | 0.0433% | 2,308 |
| South Asian | 0.0022% | 45,544 |
| European (non-Finnish) | 0.00102% | 98,329 |
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.Thr109=
- Coding
- c.327G>A
- MANE Select
- NM_001378789
- dbSNP
- rs115592596
- Type
- single nucleotide variant
- Location
- chr15:100484630 (GRCh38)
- Gene constraint
- LOEUF 1.14 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.52
- Residue 109
- the 'homeobox-like' 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-thr109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown