STRN4 p.Pro158=
c.474C>T · rs115934734 · VCV785629
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.51%, afr)
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 -9.3 | GERP -2.8 |
| Overall | ||
| CADD | 0.737 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.51%
African / African-American · 3,378/74,840 alleles
Filtering AF
4.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.33%
Overall
0.277%
4,472/1,611,980 alleles · low-frequency
exomes 2,476/1,459,778 · genomes 1,996/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.51% | 22 |
| Admixed American | 0.381% | 262 |
| Remaining individualsnot grpmax-eligible | 0.349% | 286 |
| Middle Eastern | 0.116% | 865 |
| European (non-Finnish) | 0.0534% | 1,871 |
| South Asian | 0.011% | 9,078 |
| East Asian | 0.00224% | 44,596 |
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
- STRN4
- Protein
- p.Pro158=
- Coding
- c.474C>T
- MANE Select
- NM_013403
- dbSNP
- rs115934734
- Type
- single nucleotide variant
- Location
- chr19:46736888 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 68.59
Similar variants
- FKRP c.-253+4A>G Uncertain significance ★★ same type
- FKRP c.-253+5G>A Uncertain significance ★★ same type
- FKRP c.-272G>A Conflicting classifications of pathogenicity ★ same type
- STRN4 c.1154-14T>G Uncertain significance ★ same type
- STRN4 c.1154-7T>C Uncertain significance ★ same type
- STRN4 c.1907-1G>T Uncertain significance ★ same type
- STRN4 c.737+1G>C Uncertain significance ★ same type
- STRN4 p.Ala124Val 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/strn4-p-pro158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown