SAG p.Ala196=
c.588G>A · rs190853693 · VCV712453
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.646%, afr)
Conditions
2
Oguchi disease
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 -5 | GERP -3.5 |
| Overall | ||
| CADD | 6.599 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.646%
African / African-American · 485/75,056 alleles
Filtering AF
0.599%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.58%
Overall
0.0352%
568/1,613,916 alleles · rare
exomes 262/1,461,616 · genomes 306/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.646% | 155 |
| Remaining individualsnot grpmax-eligible | 0.0672% | 1,488 |
| Admixed American | 0.0483% | 2,069 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 0.000763% | 131,093 |
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
- SAG
- Protein
- p.Ala196=
- Coding
- c.588G>A
- MANE Select
- NM_000541
- dbSNP
- rs190853693
- Type
- single nucleotide variant
- Location
- chr2:233328553 (GRCh38)
- Structure
- AlphaFold pLDDT 83.02 · 7 PDB
Similar variants
- SAG p.Ala196Val Uncertain significance ★★ ⚠ same residue
- SAG p.Ala196Glu Uncertain significance ★ ⚠ same residue
- SAG c.1103-2A>C Pathogenic/Likely pathogenic ★★ same condition
- SAG c.136+2T>G Pathogenic/Likely pathogenic ★★ same condition
- SAG p.Arg193Ter Pathogenic ★★ same condition
- SAG p.Arg292Ter Pathogenic ★★ same condition
- SAG p.Gln191Ter Pathogenic/Likely pathogenic ★★ same condition
- SAG c.944+5G>A Uncertain significance ★★ 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/sag-p-ala196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown