DPP4 p.Lys539=
c.1617A>G · rs72868637 · VCV732560
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.11%, 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 1.9 | GERP 0.22, phastCons 1 |
| Overall | ||
| CADD | 10.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.11%
European (non-Finnish) · 1,296/1,176,694 alleles
Filtering AF
0.105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.103%
Overall
0.0857%
1,378/1,608,246 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.11% | 908 |
| Remaining individualsnot grpmax-eligible | 0.0675% | 1,482 |
| Finnishnot grpmax-eligible | 0.0437% | 2,286 |
| South Asian | 0.00554% | 18,052 |
| African / African-American | 0.00535% | 18,706 |
| Admixed American | 0.00508% | 19,686 |
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.Lys539=
- Coding
- c.1617A>G
- MANE Select
- NM_001935
- dbSNP
- rs72868637
- Type
- single nucleotide variant
- Location
- chr2:162014416 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.45 · 121 PDB
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.Ser437Thr Benign ★★ ⚠ same type
- DPP4 p.Val266Ile Likely benign ★★ ⚠ same type
- DPP4 p.Ala654Thr Uncertain significance ★ ⚠ same type
- DPP4 p.Ala81Thr 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-lys539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown