CSAD p.Glu50=
c.150G>A · rs148549862 · VCV791052
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.06%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.471 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -2.5, phastCons 0.48 |
| Overall | ||
| CADD | 7.871 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.06%
South Asian · 951/90,052 alleles
Filtering AF
1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.978%
Overall
0.487%
7,827/1,608,592 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.06% | 95 |
| Ashkenazi Jewishnot grpmax-eligible | 0.872% | 115 |
| Middle Eastern | 0.794% | 126 |
| Finnishnot grpmax-eligible | 0.673% | 149 |
| Remaining individualsnot grpmax-eligible | 0.567% | 176 |
| European (non-Finnish) | 0.457% | 219 |
| Admixed American | 0.337% | 297 |
| African / African-American | 0.279% | 358 |
| East Asian | 0.00224% | 44,608 |
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.Glu50=
- Coding
- c.150G>A
- MANE Select
- NM_001244705
- dbSNP
- rs148549862
- Type
- single nucleotide variant
- Location
- chr12:53172625 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.67 · 1 PDB
- Residue 50
- an α-helix
Similar variants
- CSAD p.Ala103= Benign ★★ same type
- CSAD p.Ala199= 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
- CSAD c.-48A>G Uncertain significance ★ same type
- CSAD c.-90-660A>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-glu50 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown