DPT p.Phe130=
c.390T>C · rs570509194 · VCV726434
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.191%, sas)
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 0.61 | GERP -4.7, phastCons 0.93 |
| Overall | ||
| CADD | 6.396 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.191%
South Asian · 174/91,076 alleles
Filtering AF
0.168%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.159%
Overall
0.112%
1,803/1,614,048 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.191% | 523 |
| European (non-Finnish) | 0.127% | 785 |
| Remaining individualsnot grpmax-eligible | 0.102% | 977 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,974 |
| Middle Eastern | 0.033% | 3,031 |
| Admixed American | 0.0317% | 3,158 |
| African / African-American | 0.0187% | 5,356 |
| Finnishnot grpmax-eligible | 0.0172% | 5,821 |
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.Phe130=
- Coding
- c.390T>C
- MANE Select
- NM_001937
- dbSNP
- rs570509194
- Type
- single nucleotide variant
- Location
- chr1:168714262 (GRCh38)
- Gene constraint
- LOEUF 0.963 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.21
- Residue 130
- a disulfide bond; the '2 x 53-55 aa tandem repeats' region; the '3 x 6 aa repeats of d-r-[eq]-w-[nqk]-[fy]' region
Similar variants
- DPT p.Ala58= 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-phe130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown