DPT p.Ala58=
c.174C>A · rs139513961 · VCV790493
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.25%, 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 -4.5 | GERP -3.7 |
| Overall | ||
| CADD | 3.291 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.25%
African / African-American · 1,691/75,028 alleles
Filtering AF
2.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.13%
Overall
0.115%
1,854/1,614,128 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.25% | 44 |
| Remaining individualsnot grpmax-eligible | 0.147% | 679 |
| Admixed American | 0.095% | 1,053 |
| Middle Eastern | 0.066% | 1,516 |
| South Asian | 0.00439% | 22,769 |
| European (non-Finnish) | 0.000508% | 196,670 |
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
- DPT
- Protein
- p.Ala58=
- Coding
- c.174C>A
- MANE Select
- NM_001937
- dbSNP
- rs139513961
- Type
- single nucleotide variant
- Location
- chr1:168729001 (GRCh38)
- Gene constraint
- LOEUF 0.963 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.21
- Residue 58
- a disulfide bond; the '2 x 53-55 aa tandem repeats' region
Similar variants
- DPT p.Phe130= Likely benign ★★ same type
- DPT p.Ser83Ile Likely benign ★★ same type
- DPT p.Tyr194= Benign ★★ same type
- DPT p.Val201Ile Benign ★★ same type
- DPT p.Arg126Gln Uncertain significance ★ ⚠ same type
- DPT p.Arg134Cys Uncertain significance ★ ⚠ same type
- DPT p.Arg134His Uncertain significance ★ ⚠ same type
- DPT p.Arg182Cys Conflicting classifications of pathogenicity ★ 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/dpt-p-ala58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown