DPP6 p.Leu44=
c.132C>T · rs866677381 · VCV2658248
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0894%, 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 -0.28 | GERP 0.96 |
| Overall | ||
| CADD | 7.689 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0894%
African / African-American · 56/62,664 alleles
Filtering AF
0.0706%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0639%
Overall
0.00853%
104/1,218,520 alleles · ultra-rare
exomes 62/1,071,032 · genomes 42/147,488 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0894% | 1,119 |
| Middle Eastern | 0.0632% | 1,582 |
| Admixed American | 0.0388% | 2,579 |
| Remaining individualsnot grpmax-eligible | 0.0213% | 4,701 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00533% | 18,776 |
| European (non-Finnish) | 0.00259% | 38,682 |
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.Leu44=
- Coding
- c.132C>T
- MANE Select
- NM_130797
- dbSNP
- rs866677381
- Type
- single nucleotide variant
- Location
- chr7:154052952 (GRCh38)
- Gene constraint
- LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.41 · 8 PDB
- Residue 44
- the 'disordered' region
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-leu44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown