DPP9 p.Pro322=
c.966T>C · rs74793100 · VCV779179
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.59%, afr) — too common for a highly-penetrant pathogenic allele
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 -6.2 | GERP -3.6 |
| Overall | ||
| CADD | 0.059 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.59%
African / African-American · 4,944/75,008 alleles
Filtering AF
6.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.38%
Overall
0.358%
5,775/1,613,916 alleles · common
exomes 2,970/1,461,636 · genomes 2,805/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.59% | 15 |
| Remaining individualsnot grpmax-eligible | 0.493% | 203 |
| Admixed American | 0.48% | 208 |
| Middle Eastern | 0.462% | 216 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0608% | 1,645 |
| South Asian | 0.0165% | 6,072 |
| European (non-Finnish) | 0.0147% | 6,820 |
| East Asian | 0.00223% | 44,880 |
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
- DPP9
- Protein
- p.Pro322=
- Coding
- c.966T>C
- MANE Select
- NM_139159
- dbSNP
- rs74793100
- Type
- single nucleotide variant
- Location
- chr19:4702073 (GRCh38)
- Gene constraint
- LOEUF 0.647 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.96 · 14 PDB
- Residue 322
- a UniProt-annotated variant site (in hatis; likely pathogenic); a β-strand
Similar variants
- DPP9 p.Asp310Asn Uncertain significance ★★ ⚠ same type
- DPP9 p.Lys509Arg Uncertain significance ★★ ⚠ same type
- DPP9 p.Thr301Met Uncertain significance ★★ ⚠ same type
- DPP9 p.Ala184Gly Benign/Likely benign ★★ same type
- DPP9 p.Glu566Lys Benign/Likely benign ★★ same type
- DPP9 p.His83= Benign/Likely benign ★★ same type
- DPP9 p.Ser236Asn Likely benign ★★ same type
- DPP9 p.Thr329Met Benign ★★ 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/dpp9-p-pro322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown