STRC p.Lys1420=
c.4260G>A · rs140545217 · VCV227968
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.035%, mid)
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 -0.24 | GERP -2.4, phastCons 0.21 |
| Overall | ||
| CADD | 3.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.035%
Middle Eastern · 2/5,722 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.00385%
62/1,611,738 alleles · ultra-rare
exomes 48/1,459,808 · genomes 14/151,930 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.035% | 2,861 |
| African / African-American | 0.016% | 6,244 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,795 |
| East Asian | 0.00446% | 22,422 |
| Admixed American | 0.00334% | 29,955 |
| European (non-Finnish) | 0.00305% | 32,744 |
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
- STRC
- Protein
- p.Lys1420=
- Coding
- c.4260G>A
- MANE Select
- NM_153700
- dbSNP
- rs140545217
- Type
- single nucleotide variant
- Location
- chr15:43604111 (GRCh38)
- Gene constraint
- LOEUF 0.713 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.21
Similar variants
- STRC c.4219-1G>A Pathogenic/Likely pathogenic ★★ same type
- STRC c.4701+1G>A Pathogenic/Likely pathogenic ★★ same type
- STRC p.Arg1073Ter Pathogenic ★★ same type
- STRC p.Arg1154Ter Pathogenic/Likely pathogenic ★★ same type
- STRC p.Arg1224Ter Pathogenic ★★ same type
- STRC p.Arg1338Ter Pathogenic/Likely pathogenic ★★ same type
- STRC p.Arg1451Ter Pathogenic/Likely pathogenic ★★ same type
- STRC p.Arg1468Ter Pathogenic ★★ 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/strc-p-lys1420 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown