ACSS2 p.Lys342=
c.1026G>A · rs60867847 · VCV3043271
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.522%, afr)
Conditions
1
ACSS2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.7 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 15.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.522%
African / African-American · 392/75,068 alleles
Filtering AF
0.479%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.463%
Overall
0.03%
485/1,614,226 alleles · rare
exomes 269/1,461,868 · genomes 216/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.522% | 192 |
| Middle Eastern | 0.148% | 674 |
| Remaining individualsnot grpmax-eligible | 0.0656% | 1,525 |
| Admixed American | 0.015% | 6,670 |
| South Asian | 0.0143% | 7,007 |
| European (non-Finnish) | 0.00178% | 56,192 |
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.Lys342=
- Coding
- c.1026G>A
- MANE Select
- NM_018677
- dbSNP
- rs60867847
- Type
- single nucleotide variant
- Location
- chr20:34920592 (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.Pro486= 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-lys342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown