DNM3 p.Pro263=
c.789G>A · rs749873284 · VCV2639557
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00337%, amr)
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 -1.2 | GERP -4.1 |
| Overall | ||
| CADD | 8.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00337%
Admixed American · 2/59,302 alleles
Filtering AF
0.0024%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0021%
Overall
0.00267%
43/1,608,654 alleles · very rare
exomes 41/1,456,600 · genomes 2/152,054 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00337% | 29,651 |
| European (non-Finnish) | 0.00323% | 30,989 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,143 |
| South Asian | 0.00111% | 89,814 |
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
- DNM3
- Protein
- p.Pro263=
- Coding
- c.789G>A
- MANE Select
- NM_015569
- dbSNP
- rs749873284
- Type
- single nucleotide variant
- Location
- chr1:172033205 (GRCh38)
- Gene constraint
- LOEUF 0.689 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.06 · 2 PDB
- Residue 263
- the dynamin-type g domain; a turn
Similar variants
- DNM3 p.Pro263Leu Uncertain significance ★ ⚠ same residue
- DNM3 p.Arg290Gln Uncertain significance ★★ ⚠ same type
- DNM3 p.Asn686= Benign ★★ same type
- DNM3 p.Thr833= Benign ★★ same type
- DNM3 p.Ala19Val Uncertain significance ★ same type
- DNM3 p.Ala254Ser Uncertain significance ★ ⚠ same type
- DNM3 p.Ala254Thr Uncertain significance ★ ⚠ same type
- DNM3 p.Ala313Thr 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/dnm3-p-pro263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown