GSN p.Ser262=
c.786C>T · rs546357006 · VCV738621
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.253%, 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 0.35 | GERP -0.29, phastCons 0.99 |
| Overall | ||
| CADD | 8.468 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.253%
South Asian · 230/91,084 alleles
Filtering AF
0.226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.215%
Overall
0.0164%
264/1,614,194 alleles · rare
exomes 241/1,461,874 · genomes 23/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.253% | 396 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,718 |
| Middle Eastern | 0.033% | 3,031 |
| African / African-American | 0.0107% | 9,381 |
| East Asian | 0.00223% | 44,878 |
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
- GSN
- Protein
- p.Ser262=
- Coding
- c.786C>T
- MANE Select
- NM_198252
- dbSNP
- rs546357006
- Type
- single nucleotide variant
- Location
- chr9:121317118 (GRCh38)
- Gene constraint
- LOEUF 0.788 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.76 · 65 PDB
- Residue 262
- the 'disordered' region; a β-strand
Similar variants
- GSN p.Asn160Lys Pathogenic ★★ same type
- GSN p.Asp163Asn Pathogenic/Likely pathogenic ★★ same type
- GSN p.Asp163Tyr Pathogenic/Likely pathogenic ★★ same type
- GSN c.1762+2T>C Uncertain significance ★★ same type
- GSN c.513+1G>A Uncertain significance ★★ same type
- GSN c.753+1G>A Uncertain significance ★★ same type
- GSN c.754-1G>T Uncertain significance ★★ same type
- GSN c.-9-1981C>T 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/gsn-p-ser262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown