DPP3 p.Phe331=
c.993C>T · rs17849480 · VCV786199
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.8%, 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 -9.5 | GERP -4.8 |
| Overall | ||
| CADD | 2.449 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.8%
African / African-American · 2,815/74,014 alleles
Filtering AF
3.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.64%
Overall
0.212%
3,356/1,585,064 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.8% | 26 |
| Admixed American | 0.238% | 421 |
| Remaining individualsnot grpmax-eligible | 0.229% | 437 |
| Middle Eastern | 0.119% | 842 |
| European (non-Finnish) | 0.0215% | 4,649 |
| South Asian | 0.0139% | 7,185 |
| East Asian | 0.00224% | 44,652 |
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
- DPP3
- Protein
- p.Phe331=
- Coding
- c.993C>T
- MANE Select
- NM_130443
- dbSNP
- rs17849480
- Type
- single nucleotide variant
- Location
- chr11:66492720 (GRCh38)
- Gene constraint
- LOEUF 0.827 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.56 · 10 PDB
- Residue 331
- a β-strand
Similar variants
- DPP3 p.Arg76His Benign ★★ ⚠ same type
- DPP3 p.Leu163Met Benign ★★ ⚠ same type
- DPP3 p.Lys423= Benign ★★ same type
- DPP3 p.Phe443= Benign ★★ same type
- DPP3 p.Thr401= Benign ★★ same type
- DPP3 c.573+1G>A Uncertain significance ★ same type
- DPP3 p.Ala22Gly Uncertain significance ★ ⚠ same type
- DPP3 p.Ala22Thr 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/dpp3-p-phe331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown