DST p.Arg56His
c.167G>A · rs1037693066 · VCV1777878
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00675%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.412 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.4, phastCons 1 |
| Regional constraint | o/e 0.81 | unconstrained · MANE · 320 kb · p 2.5e-12 · regional, not allelic |
| Overall | ||
| CADD | 26.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00675%
European (non-Finnish) · 69/1,021,574 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00497%
Overall
0.00527%
72/1,366,810 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00675% | 14,805 |
| Remaining individualsnot grpmax-eligible | 0.00434% | 23,034 |
| African / African-American | 0.00148% | 67,718 |
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.Arg56His
- Coding
- c.167G>A
- MANE Select
- NM_001374736
- dbSNP
- rs1037693066
- Type
- single nucleotide variant
- Location
- chr6:56954421 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
- Residue 56
- the calponin-homology (ch) 1 domain; the 'actin-binding' region
Similar variants
- DST p.Gln4023Ter Pathogenic/Likely pathogenic ★★ same condition
- DST c.16770+5T>C Uncertain significance ★★ same condition
- DST c.17269-3T>A Uncertain significance ★★ same condition
- DST c.18129+3A>G Uncertain significance ★★ same condition
- DST c.182-5C>T Uncertain significance ★★ same condition
- DST c.19896+4C>T Uncertain significance ★★ same condition
- DST c.20551-3A>C Uncertain significance ★★ same condition
- DST c.22959+3A>G Uncertain significance ★★ 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-arg56his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown