DNAJC3 p.Asp466=
c.1398T>C · rs746076866 · VCV3050332
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0095%, nfe)
Conditions
1
DNAJC3-related disorder
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 -2.4 | GERP -5.9 |
| Overall | ||
| CADD | 4.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0095%
European (non-Finnish) · 112/1,178,524 alleles
Filtering AF
0.00805%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00753%
Overall
0.00716%
115/1,606,932 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0095% | 10,523 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,106 |
| South Asian | 0.00112% | 89,174 |
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
- DNAJC3
- Protein
- p.Asp466=
- Coding
- c.1398T>C
- MANE Select
- NM_006260
- dbSNP
- rs746076866
- Type
- single nucleotide variant
- Location
- chr13:95790913 (GRCh38)
- Gene constraint
- LOEUF 0.738 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.78 · 2 PDB
- Residue 466
- the 'disordered' region
Disease context
DNAJC3-related disorder
Similar variants
- DNAJC3 p.Asp466Ala Uncertain significance ★ ⚠ same residue
- DNAJC3 p.Arg393Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAJC3 c.729-3C>T Likely benign same condition
- DNAJC3 p.Asp441Glu Likely benign ⚠ same condition
- DNAJC3 p.Val37= Likely benign same condition
- DNAJC3 p.Asp69Gly Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Leu231Val Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Ser450Cys 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/dnajc3-p-asp466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown