ACSS2 p.Pro486=
c.1458C>T · rs58314413 · VCV3053292
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.495%, eas)
Conditions
1
ACSS2-related disorder
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 1.9 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 13.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.495%
East Asian · 222/44,882 alleles
Filtering AF
0.441%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.421%
Overall
0.0167%
269/1,614,204 alleles · rare
exomes 251/1,461,894 · genomes 18/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.495% | 202 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| African / African-American | 0.00267% | 37,523 |
| Admixed American | 0.00167% | 60,028 |
| European (non-Finnish) | 0.0011% | 90,772 |
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
- ACSS2
- Protein
- p.Pro486=
- Coding
- c.1458C>T
- MANE Select
- NM_018677
- dbSNP
- rs58314413
- Type
- single nucleotide variant
- Location
- chr20:34921591 (GRCh38)
- Gene constraint
- LOEUF 0.785 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.14
Disease context
ACSS2-related disorder
Similar variants
- ACSS2 p.Arg153Gln Uncertain significance ⚠ same condition
- ACSS2 p.Arg696His Uncertain significance same condition
- ACSS2 p.Ala307= Likely benign same condition
- ACSS2 p.Asp309= Likely benign same condition
- ACSS2 p.His252= Benign same condition
- ACSS2 p.Lys342= Likely benign same condition
- ACSS2 p.Thr137= Likely benign same condition
- ACSS2 p.Thr628= Likely benign same condition
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/acss2-p-pro486 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown