DPP10 p.His130=
c.390T>C · rs138259404 · VCV715475
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.237%, nfe)
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 0.2 | GERP 0.4, phastCons 0.99 |
| Overall | ||
| CADD | 7.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.237%
European (non-Finnish) · 2,792/1,178,302 alleles
Filtering AF
0.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.227%
Overall
0.187%
3,008/1,609,716 alleles · rare
exomes 2,814/1,457,552 · genomes 194/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.237% | 422 |
| Remaining individualsnot grpmax-eligible | 0.117% | 854 |
| Finnishnot grpmax-eligible | 0.105% | 954 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0644% | 1,552 |
| African / African-American | 0.0414% | 2,415 |
| Admixed American | 0.0336% | 2,980 |
| South Asian | 0.00773% | 12,929 |
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
- DPP10
- Protein
- p.His130=
- Coding
- c.390T>C
- MANE Select
- NM_020868
- dbSNP
- rs138259404
- Type
- single nucleotide variant
- Location
- chr2:115525921 (GRCh38)
- Gene constraint
- LOEUF 0.378 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.67 · 1 PDB
- Residue 130
- a β-strand
Similar variants
- DPP10 p.Asp380= Benign ★★ same type
- DPP10 p.Glu234Asp Benign ★★ same type
- DPP10 p.Gly601Ser Benign ★★ same type
- DPP10 p.Leu575= Benign ★★ same type
- DPP10 c.852+1G>T Uncertain significance ★ same type
- DPP10 p.Ala112Ser Uncertain significance ★ ⚠ same type
- DPP10 p.Ala455Val Uncertain significance ★ ⚠ same type
- DPP10 p.Ala726Ser Uncertain significance ★ ⚠ 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/dpp10-p-his130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown