CSAD p.Arg389=
c.1167G>A · rs745653871 · VCV3077945
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0612%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.141 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.62 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 15.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0612%
Admixed American · 36/58,844 alleles
Filtering AF
0.0454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0399%
Overall
0.00243%
39/1,606,256 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0612% | 1,635 |
| South Asian | 0.00222% | 44,992 |
| European (non-Finnish) | 8.5e-05% | 1,175,814 |
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
- CSAD
- Protein
- p.Arg389=
- Coding
- c.1167G>A
- MANE Select
- NM_001244705
- dbSNP
- rs745653871
- Type
- single nucleotide variant
- Location
- chr12:53159938 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.67 · 1 PDB
- Residue 389
- an α-helix
Similar variants
- CSAD p.Arg389Trp Uncertain significance ★ ⚠ same residue
- CSAD p.Ala103= Benign ★★ same type
- CSAD p.Ala199= Benign ★★ same type
- CSAD p.Glu50= Benign ★★ same type
- CSAD c.-21C>T Uncertain significance ★ same type
- CSAD c.-24G>T Uncertain significance ★ same type
- CSAD c.-27C>T Uncertain significance ★ same type
- CSAD c.-33C>G 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/csad-p-arg389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown