CERS6 p.Arg57=
c.171A>G · rs780317964 · VCV2590084
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0988%, mid)
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 1.3 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 9.512 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0988%
Middle Eastern · 6/6,070 alleles
Filtering AF
0.0654%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0599%
Overall
0.00851%
137/1,610,480 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0988% | 1,012 |
| South Asian | 0.0802% | 1,246 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,470 |
| European (non-Finnish) | 0.0045% | 22,207 |
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
- CERS6
- Protein
- p.Arg57=
- Coding
- c.171A>G
- MANE Select
- NM_203463
- dbSNP
- rs780317964
- Type
- single nucleotide variant
- Location
- chr2:168547596 (GRCh38)
- Gene constraint
- LOEUF 0.593 · pLI 0.43 (gnomAD)
- Structure
- AlphaFold pLDDT 87.97 · 3 PDB
- Residue 57
- an α-helix
Similar variants
- CERS6 p.Ala30Ser Uncertain significance ★ ⚠ same type
- CERS6 p.Ala326Val Uncertain significance ★ ⚠ same type
- CERS6 p.Ala362Val Uncertain significance ★ ⚠ same type
- CERS6 p.Ala6Val Uncertain significance ★ ⚠ same type
- CERS6 p.Arg121Cys Uncertain significance ★ ⚠ same type
- CERS6 p.Asn10Lys Uncertain significance ★ ⚠ same type
- CERS6 p.Asn122Ser Uncertain significance ★ ⚠ same type
- CERS6 p.Asn168Lys 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/cers6-p-arg57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown