DPP6 c.243+13del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 44.7%, 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 +13 | near-intronic (+13 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.088 | GERP -5.2 |
| Overall | ||
| CADD | 5.361 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
44.7%
East Asian · 6,807/15,240 alleles
Filtering AF
43.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 43.4%
Overall
24.6%
257,549/1,047,750 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 44.7% | 2 |
| South Asian | 27.6% | 4 |
| Admixed American | 26.8% | 4 |
| African / African-American | 26% | 4 |
| Remaining individualsnot grpmax-eligible | 24.5% | 4 |
| European (non-Finnish) | 24.2% | 4 |
| Middle Eastern | 23.6% | 4 |
| Amishnot grpmax-eligible | 21.8% | 5 |
| Finnishnot grpmax-eligible | 21.5% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 17.8% | 6 |
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.243+13del
- MANE Select
- NM_130797
- dbSNP
- rs199977459
- Type
- Deletion
- Location
- chr7:154053076 (GRCh38)
- Gene constraint
- LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.41 · 8 PDB
Similar variants
- DPP6 c.627+20964_627+20966del Uncertain significance ★ same type
- DPP6 p.Asp865fs Uncertain significance ★ same type
- DPP6 p.Pro53fs Conflicting classifications of pathogenicity ★ same type
- DPP6 c.1136+40del Benign ★ same type
- DPP6 c.1261-48_1261-40del Benign ★ same type
- DPP6 c.51+164380_51+164383del Benign ★ same type
- DPP6 c.-88del Benign ★ same type
- DPP6 c.49_51+7del 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/dpp6-c-243-plus-13del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown