STRN4 p.Thr628=
c.1884G>A · rs149490274 · VCV782346
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.737%, afr)
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 -4.4 | GERP -3.6 |
| Overall | ||
| CADD | 6.355 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.737%
African / African-American · 553/75,072 alleles
Filtering AF
0.686%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.666%
Overall
0.0547%
883/1,613,906 alleles · rare
exomes 544/1,461,540 · genomes 339/152,366 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.737% | 136 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,078 |
| Admixed American | 0.0733% | 1,364 |
| Middle Eastern | 0.066% | 1,516 |
| European (non-Finnish) | 0.0188% | 5,315 |
| East Asian | 0.00223% | 44,888 |
| South Asian | 0.0011% | 91,088 |
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.Thr628=
- Coding
- c.1884G>A
- MANE Select
- NM_013403
- dbSNP
- rs149490274
- Type
- single nucleotide variant
- Location
- chr19:46722832 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 68.59
Similar variants
- STRN4 p.Thr628Met Uncertain significance ★ ⚠ same residue
- FKRP c.-253+4A>G Uncertain significance ★★ same type
- FKRP c.-253+5G>A Uncertain significance ★★ same type
- STRN4 p.Pro158= Benign ★★ 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
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-thr628 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown