SAG p.Pro262=
c.786C>T · rs565335757 · VCV1083829
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0264%, sas)
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 -10 | GERP -3.5 |
| Overall | ||
| CADD | 0.135 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0264%
South Asian · 24/91,018 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.00248%
40/1,613,556 alleles · ultra-rare
exomes 31/1,461,268 · genomes 9/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0264% | 3,792 |
| Admixed American | 0.00833% | 12,000 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,825 |
| African / African-American | 0.00133% | 75,030 |
| European (non-Finnish) | 0.000593% | 168,511 |
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.Pro262=
- Coding
- c.786C>T
- MANE Select
- NM_000541
- dbSNP
- rs565335757
- Type
- single nucleotide variant
- Location
- chr2:233331692 (GRCh38)
- Structure
- AlphaFold pLDDT 83.02 · 7 PDB
Similar variants
- SAG c.1023-2A>G Likely pathogenic ★★ same type
- SAG c.1103-2A>C Pathogenic/Likely pathogenic ★★ same type
- SAG c.136+2T>C Likely pathogenic ★★ same type
- SAG c.136+2T>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.181+1G>A Likely pathogenic ★★ same type
- SAG c.182-2A>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.376-2A>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.435+1G>A Likely pathogenic ★★ 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/sag-p-pro262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown