DNM1L p.Ser694=
c.2082C>T · rs370363569 · VCV380443
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0108%, 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 -0.17 | phastCons 0.21 |
| Overall | ||
| CADD | 8.424 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0108%
European (non-Finnish) · 128/1,180,010 alleles
Filtering AF
0.00928%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00871%
Overall
0.00836%
135/1,613,870 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0108% | 9,219 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,496 |
| Admixed American | 0.00333% | 29,987 |
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
- DNM1L
- Protein
- p.Ser694=
- Coding
- c.2082C>T
- MANE Select
- NM_012062
- dbSNP
- rs370363569
- Type
- single nucleotide variant
- Location
- chr12:32742676 (GRCh38)
- Gene constraint
- LOEUF 0.506 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 77.09 · 11 PDB
- Residue 694
- an α-helix; the ged domain
Similar variants
- DNM1L c.1596+2T>A Likely pathogenic ★★ same type
- DNM1L c.1674+1G>A Pathogenic/Likely pathogenic ★★ same type
- DNM1L p.Arg403Cys Pathogenic ★★ same type
- DNM1L p.Arg530Ter Pathogenic/Likely pathogenic ★★ same type
- DNM1L p.Asp146Asn Pathogenic/Likely pathogenic ★★ same type
- DNM1L p.Cys431Tyr Pathogenic ★★ same type
- DNM1L p.Gly362Ser Pathogenic ★★ same type
- DNM1L p.Gly401Ser Likely pathogenic ★★ 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/dnm1l-p-ser694 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown