DST p.Leu1744Met
c.5230C>A · rs75752366 · VCV1057943
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.178%, afr)
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.071 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP -0.91, phastCons 1 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 36 kb · p 0.7 · regional, not allelic |
| Overall | ||
| CADD | 21.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.178%
African / African-American · 132/74,010 alleles
Filtering AF
0.154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.144%
Overall
0.0088%
138/1,568,100 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.178% | 561 |
| Remaining individualsnot grpmax-eligible | 0.00658% | 15,201 |
| Admixed American | 0.00374% | 26,716 |
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.Leu1744Met
- Coding
- c.5230C>A
- MANE Select
- NM_001374736
- dbSNP
- rs75752366
- Type
- single nucleotide variant
- Location
- chr6:56610480 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
Similar variants
- DST c.22959+1G>A Likely pathogenic ★★ same condition
- DST p.Arg1512Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Arg22Ter Likely pathogenic ★★ same condition
- DST p.Arg7329Ter Pathogenic ★★ same condition
- DST p.Cys1828Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Gln1124Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Gln1366Ter Pathogenic/Likely pathogenic ★★ same condition
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-leu1744met (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown