DPF2 p.Thr102=
c.306A>G · rs370514099 · VCV2715145
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00534%, nfe)
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 0.54 | GERP -0.5, phastCons 0.88 |
| Overall | ||
| CADD | 8.765 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
European (non-Finnish) · 63/1,180,034 alleles
Filtering AF
0.00426%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00387%
Overall
0.00409%
66/1,614,090 alleles · very rare
exomes 63/1,461,870 · genomes 3/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00534% | 18,731 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
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.Thr102=
- Coding
- c.306A>G
- MANE Select
- NM_006268
- dbSNP
- rs370514099
- Type
- single nucleotide variant
- Location
- chr11:65341403 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.62 · 9 PDB
- Residue 102
- the 'disordered' region
Similar variants
- DPF2 p.Thr102Ile 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-thr102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown