DPP6 p.Thr694=
c.2082G>A · rs183375220 · VCV3250722
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.68%, eas)
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 -1.2 | GERP -2.9 |
| Overall | ||
| CADD | 2.892 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.68%
East Asian · 305/44,868 alleles
Filtering AF
0.617%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.592%
Overall
0.0245%
396/1,613,978 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.68% | 147 |
| Remaining individualsnot grpmax-eligible | 0.0688% | 1,453 |
| South Asian | 0.0231% | 4,337 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.015% | 6,668 |
| European (non-Finnish) | 0.00136% | 73,744 |
| African / African-American | 0.00133% | 75,042 |
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
- DPP6
- Protein
- p.Thr694=
- Coding
- c.2082G>A
- MANE Select
- NM_130797
- dbSNP
- rs183375220
- Type
- single nucleotide variant
- Location
- chr7:154880891 (GRCh38)
- Gene constraint
- LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.41 · 8 PDB
- Residue 694
- an α-helix
Similar variants
- DPP6 p.Gly65Cys Uncertain significance ★★ ⚠ same type
- DPP6 p.Gly65Val Uncertain significance ★★ ⚠ same type
- DPP6 p.Lys223Arg Uncertain significance ★★ ⚠ same type
- DPP6 p.Pro229Thr Uncertain significance ★★ ⚠ same type
- DPP6 c.1261-188G>A Benign ★★ same type
- DPP6 c.1261-48G>A Benign ★★ same type
- DPP6 c.1299+147A>G Benign ★★ same type
- DPP6 c.1299+200A>G 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/dpp6-p-thr694 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown