DEF6 c.237+14del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +14 | near-intronic (+14 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.085 | GERP -1.9 |
| Non-coding constraint | Z 2.44 | 1 kb window · o/e 0.82 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,550 alleles
Overall
6.84e-05%
1/1,461,150 alleles · very rare
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
- DEF6
- Coding
- c.237+14del
- MANE Select
- NM_022047
- Type
- Deletion
- Location
- chr6:35309823 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.91
Similar variants
- DEF6 p.Leu159fs Likely pathogenic ★ same type
- DEF6 p.Leu179fs Pathogenic ★ same type
- DEF6 p.Leu271fs Pathogenic ★ same type
- DEF6 p.Lys74fs Pathogenic ★ same type
- DEF6 c.1383-11_1383-8del Uncertain significance ★ same type
- DEF6 p.Glu169_Gln171del 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/def6-c-237-plus-14del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown