DPP9 p.Asp193=
c.579C>T · rs187492097 · VCV3250611
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.18%, 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 -6.1 | GERP -3.5 |
| Overall | ||
| CADD | 1.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.18%
African / African-American · 884/75,056 alleles
Filtering AF
1.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.09%
Overall
0.0687%
1,109/1,613,962 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.18% | 85 |
| Admixed American | 0.165% | 606 |
| Remaining individualsnot grpmax-eligible | 0.0944% | 1,059 |
| Middle Eastern | 0.0825% | 1,212 |
| European (non-Finnish) | 0.00509% | 19,665 |
| South Asian | 0.0022% | 45,544 |
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.Asp193=
- Coding
- c.579C>T
- MANE Select
- NM_139159
- dbSNP
- rs187492097
- Type
- single nucleotide variant
- Location
- chr19:4704152 (GRCh38)
- Gene constraint
- LOEUF 0.647 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.96 · 14 PDB
- Residue 193
- 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.Pro322= Benign ★★ same type
- DPP9 p.Ser236Asn Likely 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-asp193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown