DPP10 p.Asp380=
c.1140C>T · rs34741590 · VCV780833
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.55%, 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 -0.033 | GERP -4.5, phastCons 0.93 |
| Overall | ||
| CADD | 11.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.55%
African / African-American · 1,161/75,006 alleles
Filtering AF
1.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.44%
Overall
0.0964%
1,555/1,613,560 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.55% | 65 |
| Admixed American | 0.213% | 469 |
| Middle Eastern | 0.165% | 605 |
| Remaining individualsnot grpmax-eligible | 0.154% | 651 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0845% | 1,183 |
| European (non-Finnish) | 0.011% | 9,074 |
| South Asian | 0.00549% | 18,212 |
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.Asp380=
- Coding
- c.1140C>T
- MANE Select
- NM_020868
- dbSNP
- rs34741590
- Type
- single nucleotide variant
- Location
- chr2:115768323 (GRCh38)
- Gene constraint
- LOEUF 0.378 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.67 · 1 PDB
- Residue 380
- a β-strand
Similar variants
- DPP10 p.Glu234Asp Benign ★★ ⚠ same type
- DPP10 p.Gly601Ser Benign ★★ ⚠ same type
- DPP10 p.His130= Likely 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-asp380 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown