DPP9 p.Arg8Cys
c.22C>T · VCV3273656
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.095 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.6 | GERP 0.94, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 34 kb · p 0.00027 · regional, not allelic |
| Overall | ||
| CADD | 24.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,992 alleles
Filtering AF
0.000395%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000148%
Overall
0.000643%
9/1,399,394 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,992 |
| South Asian | 0.00238% | 42,032 |
| European (non-Finnish) | 0.000523% | 191,166 |
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
- DPP9
- Protein
- p.Arg8Cys
- Coding
- c.22C>T
- MANE Select
- NM_139159
- Type
- single nucleotide variant
- Location
- chr19:4719885 (GRCh38)
- Gene constraint
- LOEUF 0.647 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.96 · 14 PDB
- Residue 8
- the 'disordered' region
Similar variants
- DPP9 p.Arg8His Uncertain significance ★ same residue
- DPP9 p.Arg8Leu Uncertain significance ★ same residue
- DPP9 p.Asp310Asn Uncertain significance ★★ ⚠ same type
- DPP9 p.Lys509Arg Uncertain significance ★★ ⚠ same type
- DPP9 p.Thr301Met Uncertain significance ★★ ⚠ same type
- DPP9 p.Ala184Gly Benign/Likely benign ★★ same type
- DPP9 p.Glu566Lys Benign/Likely benign ★★ same type
- DPP9 p.His83= Benign/Likely 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/dpp9-p-arg8cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown