DPP9 p.Phe282=
c.846C>T · VCV3771399
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00383%, 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 1.8 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 9.691 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00383%
European (non-Finnish) · 45/1,175,700 alleles
Filtering AF
0.00292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0026%
Overall
0.00287%
46/1,604,138 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00383% | 26,127 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,160 |
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.Phe282=
- Coding
- c.846C>T
- MANE Select
- NM_139159
- Type
- single nucleotide variant
- Location
- chr19:4702640 (GRCh38)
- Gene constraint
- LOEUF 0.647 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.96 · 14 PDB
- Residue 282
- a UniProt-annotated variant site (in hatis; likely pathogenic); an α-helix
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-phe282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown