GSN p.Val30=
c.90G>T · rs201642174 · VCV1528018
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, amr)
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 -0.15, phastCons 1 |
| Overall | ||
| CADD | 9.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
Admixed American · 8/60,032 alleles
Filtering AF
0.00661%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.00279%
45/1,614,246 alleles · ultra-rare
exomes 37/1,461,886 · genomes 8/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0133% | 7,504 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| European (non-Finnish) | 0.0028% | 35,758 |
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.Val30=
- Coding
- c.90G>T
- MANE Select
- NM_198252
- dbSNP
- rs201642174
- Type
- single nucleotide variant
- Location
- chr9:121302061 (GRCh38)
- Gene constraint
- LOEUF 0.788 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.76 · 65 PDB
Similar variants
- GSN p.Val30Gly Uncertain significance ★ ⚠ same residue
- GSN p.Val30Met Uncertain significance ★ ⚠ same residue
- 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
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-val30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown