VSX1 p.Pro110=
c.330G>A · rs749401298 · VCV1950815
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0237%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -2 |
| Overall | ||
| CADD | 8.458 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0237%
Middle Eastern · 1/4,228 alleles
Filtering AF
0.00321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00218%
Overall
0.0006%
9/1,499,302 alleles · ultra-rare
exomes 9/1,347,030 · genomes 0/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0237% | 4,228 |
| South Asian | 0.00756% | 13,236 |
| European (non-Finnish) | 0.000177% | 566,319 |
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
- VSX1
- Protein
- p.Pro110=
- Coding
- c.330G>A
- MANE Select
- NM_014588
- dbSNP
- rs749401298
- Type
- single nucleotide variant
- Location
- chr20:25081767 (GRCh38)
- Gene constraint
- LOEUF 1.686 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.61
Similar variants
- VSX1 p.Pro110Ser Uncertain significance ★★ ⚠ same residue
- VSX1 p.Ala193Val Uncertain significance ★★ ⚠ same type
- VSX1 p.Ala256Ser Uncertain significance ★★ ⚠ same type
- VSX1 p.Ala47Thr Uncertain significance ★★ ⚠ same type
- VSX1 p.Ala94Glu Uncertain significance ★★ ⚠ same type
- VSX1 p.Cys55Ter Uncertain significance ★★ same type
- VSX1 p.Gln334Arg Uncertain significance ★★ ⚠ same type
- VSX1 p.Gly130Asp 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/vsx1-p-pro110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown