DPF2 p.Thr286=
c.858G>A · rs747337649 · VCV2974675
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.423 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -2.7 |
| Overall | ||
| CADD | 5.978 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
African / African-American · 5/74,914 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00136%
22/1,614,020 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00667% | 14,983 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| East Asian | 0.00223% | 44,878 |
| European (non-Finnish) | 0.00119% | 84,289 |
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
- DPF2
- Protein
- p.Thr286=
- Coding
- c.858G>A
- MANE Select
- NM_006268
- dbSNP
- rs747337649
- Type
- single nucleotide variant
- Location
- chr11:65346012 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.62 · 9 PDB
- Residue 286
- a turn
Similar variants
- DPF2 p.Thr286Met Uncertain significance ★ same residue
- DPF2 c.904+1G>A Pathogenic ★★ same type
- DPF2 p.Arg350His Pathogenic/Likely pathogenic ★★ same type
- DPF2 p.Asp346Asn Likely pathogenic ★★ same type
- DPF2 p.Asp349Asn Pathogenic/Likely pathogenic ★★ same type
- DPF2 p.Ala133Pro Uncertain significance ★★ ⚠ same type
- DPF2 p.Arg38His Uncertain significance ★★ ⚠ same type
- DPF2 p.Arg77Gln 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/dpf2-p-thr286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown