GSN p.Ser103=
c.309G>A · VCV3719495
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
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 -6.6 | GERP -3.8 |
| Overall | ||
| CADD | 1.982 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,180,024 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.00149%
24/1,613,746 alleles · very rare
exomes 22/1,461,590 · genomes 2/152,156 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00178% | 56,192 |
| Admixed American | 0.00167% | 60,008 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| African / African-American | 0.00134% | 74,896 |
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.Ser103=
- Coding
- c.309G>A
- MANE Select
- NM_198252
- Type
- single nucleotide variant
- Location
- chr9:121303023 (GRCh38)
- Gene constraint
- LOEUF 0.788 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.76 · 65 PDB
- Residue 103
- the 'actin-severing' region
Similar variants
- GSN p.Ser103Leu 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
- GSN c.754-1G>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-ser103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown