DST p.Lys50=
c.150A>G · rs375301517 · VCV3033992
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.5%, amr)
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 3.5 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 12.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.5%
Admixed American · 263/52,588 alleles
Filtering AF
0.45%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.431%
Overall
0.0192%
263/1,367,456 alleles · rare
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
- DST
- Protein
- p.Lys50=
- Coding
- c.150A>G
- MANE Select
- NM_001374736
- dbSNP
- rs375301517
- Type
- single nucleotide variant
- Location
- chr6:56954438 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
- Residue 50
- the calponin-homology (ch) 1 domain; the 'actin-binding' region
Similar variants
- DST c.22959+1G>A Likely pathogenic ★★ same type
- DST p.Arg1512Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Arg22Ter Likely pathogenic ★★ same type
- DST p.Arg7329Ter Pathogenic ★★ same type
- DST p.Cys1828Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Gln1124Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Gln1366Ter Pathogenic/Likely 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/dst-p-lys50 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown