CERS3 p.Asp342=
c.1026C>T · rs116101674 · VCV2018095
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.84%, amr) — too common for a highly-penetrant pathogenic allele
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 -0.48 | GERP -3.5 |
| Overall | ||
| CADD | 1.445 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.84%
Admixed American · 3,453/59,096 alleles
Filtering AF
5.68%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.61%
Overall
0.517%
8,324/1,608,880 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 5.84% | 17 |
| South Asian | 2.22% | 45 |
| Middle Eastern | 1.27% | 79 |
| East Asian | 0.878% | 114 |
| Remaining individualsnot grpmax-eligible | 0.685% | 146 |
| African / African-American | 0.565% | 177 |
| European (non-Finnish) | 0.129% | 775 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0577% | 1,734 |
| Finnishnot grpmax-eligible | 0.0173% | 5,794 |
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.Asp342=
- Coding
- c.1026C>T
- MANE Select
- NM_001378789
- dbSNP
- rs116101674
- Type
- single nucleotide variant
- Location
- chr15:100402839 (GRCh38)
- Gene constraint
- LOEUF 1.14 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.52
- Residue 342
- the 'disordered' region; a UniProt-annotated variant site (in)
Similar variants
- CERS3 p.Asp342Gly Benign ★★ same residue
- 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
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-asp342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown