SAT1 p.Arg121=
c.363C>G · rs142757578 · VCV713838
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0905%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.007 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.31 | GERP 0.69, phastCons 0.087 |
| Overall | ||
| CADD | 7.342 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0905%
Admixed American · 41/45,303 alleles
Filtering AF
0.0685%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0608%
Overall
0.0254%
306/1,206,956 alleles · ultra-rare
exomes 277/1,095,128 · genomes 29/111,828 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0905% | 1,105 |
| Middle Eastern | 0.0692% | 1,446 |
| Remaining individualsnot grpmax-eligible | 0.0505% | 1,979 |
| European (non-Finnish) | 0.0257% | 3,885 |
| African / African-American | 0.014% | 7,146 |
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
- SAT1
- Protein
- p.Arg121=
- Coding
- c.363C>G
- MANE Select
- NM_002970
- dbSNP
- rs142757578
- Type
- single nucleotide variant
- Location
- chrX:23785703 (GRCh38)
- Structure
- AlphaFold pLDDT 96.63 · 10 PDB
- Residue 121
- the n-acetyltransferase domain
Similar variants
- SAT1 p.Val129Ile 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/sat1-p-arg121 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown