CHSY1 p.Arg336=
c.1008C>T · rs777695123 · VCV727864
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, afr)
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 -6.1 | GERP -3.8 |
| Overall | ||
| CADD | 1.137 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/74,918 alleles
Filtering AF
0.00815%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00652%
Overall
0.00725%
117/1,614,070 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0147% | 6,811 |
| European (non-Finnish) | 0.00839% | 11,920 |
| East Asian | 0.00445% | 22,448 |
| South Asian | 0.00439% | 22,773 |
| Admixed American | 0.00167% | 60,006 |
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
- CHSY1
- Protein
- p.Arg336=
- Coding
- c.1008C>T
- MANE Select
- NM_014918
- dbSNP
- rs777695123
- Type
- single nucleotide variant
- Location
- chr15:101178789 (GRCh38)
- Gene constraint
- LOEUF 0.357 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 84.20
Similar variants
- CHSY1 p.Arg336Cys Uncertain significance ★★ ⚠ same residue
- CHSY1 p.Ala263Ser Uncertain significance ★★ ⚠ same type
- CHSY1 p.Ala471Thr Uncertain significance ★★ ⚠ same type
- CHSY1 p.Ala61Val Uncertain significance ★★ ⚠ same type
- CHSY1 p.Arg180His Uncertain significance ★★ ⚠ same type
- CHSY1 p.Arg229Trp Uncertain significance ★★ ⚠ same type
- CHSY1 p.Arg233Trp Uncertain significance ★★ ⚠ same type
- CHSY1 p.Arg244Trp 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/chsy1-p-arg336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown