DPP6 p.Pro470=
c.1410C>T · rs751320398 · VCV3026401
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 1.3 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 12.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.000558%
9/1,613,424 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| African / African-American | 0.00934% | 10,703 |
| European (non-Finnish) | 8.48e-05% | 1,179,632 |
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.Pro470=
- Coding
- c.1410C>T
- MANE Select
- NM_130797
- dbSNP
- rs751320398
- Type
- single nucleotide variant
- Location
- chr7:154803866 (GRCh38)
- Gene constraint
- LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.41 · 8 PDB
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-pro470 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown