DPF2 p.Leu31=
c.93C>T · VCV4751270
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0826%, 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 0.46 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 9.122 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0826%
African / African-American · 62/75,062 alleles
Filtering AF
0.066%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0601%
Overall
0.00409%
66/1,614,254 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0826% | 1,211 |
| Admixed American | 0.00333% | 30,012 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
| European (non-Finnish) | 8.47e-05% | 1,180,048 |
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.Leu31=
- Coding
- c.93C>T
- MANE Select
- NM_006268
- Type
- single nucleotide variant
- Location
- chr11:65340445 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.62 · 9 PDB
- Residue 31
- an α-helix
Similar variants
- 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
- DPF2 p.Arg83Trp 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-leu31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown