DPP6 c.680+263A>G
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 91.7%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +263 | deep intronic (+263 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.89 | GERP -1.8 |
| Non-coding constraint | Z 1.52 | 1 kb window · o/e 0.85 · regional · uncalibrated |
| Overall | ||
| CADD | 3.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
91.7%
East Asian · 4,723/5,152 alleles
Filtering AF
89.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 88.6%
Overall
75.2%
114,365/152,080 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 91.7% | 1 |
| Middle Eastern | 81.6% | 1 |
| South Asian | 80.4% | 1 |
| African / African-American | 79.5% | 1 |
| Finnishnot grpmax-eligible | 78.6% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 78.1% | 1 |
| Remaining individualsnot grpmax-eligible | 75% | 1 |
| European (non-Finnish) | 72.2% | 1 |
| Admixed American | 67.2% | 1 |
| Amishnot grpmax-eligible | 64.1% | 2 |
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
- Coding
- c.680+263A>G
- MANE Select
- NM_130797
- dbSNP
- rs1532089
- Type
- single nucleotide variant
- Location
- chr7:154638136 (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-c-680-plus-263a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown