DPP4 p.Leu415=
c.1245A>G · VCV4244486
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00139%, 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 0.17 | GERP -5.2, phastCons 0.99 |
| Overall | ||
| CADD | 6.951 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00139%
African / African-American · 1/72,112 alleles
Overall
0.000146%
2/1,372,692 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00139% | 72,112 |
| European (non-Finnish) | 9e-05% | 1,110,952 |
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
- DPP4
- Protein
- p.Leu415=
- Coding
- c.1245A>G
- MANE Select
- NM_001935
- Type
- single nucleotide variant
- Location
- chr2:162019276 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.45 · 121 PDB
- Residue 415
- a β-strand
Similar variants
- DPP4 c.1987+4T>C Benign ★★ same type
- DPP4 p.Ala16= Benign ★★ same type
- DPP4 p.Gly645= Benign ★★ same type
- DPP4 p.Leu27= Benign ★★ same type
- DPP4 p.Lys539= Likely benign ★★ same type
- DPP4 p.Ser437Thr Benign ★★ ⚠ same type
- DPP4 p.Val266Ile Likely benign ★★ ⚠ same type
- DPP4 p.Ala654Thr 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/dpp4-p-leu415 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown