DNAJC3 p.Val20=
c.60C>T · rs200556669 · VCV773036
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0828%, mid)
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 -0.51 | GERP -1.7, phastCons 0.045 |
| Overall | ||
| CADD | 9.592 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0828%
Middle Eastern · 5/6,042 alleles
Filtering AF
0.0326%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0211%
Overall
0.00175%
28/1,599,420 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0828% | 1,208 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,941 |
| Admixed American | 0.0017% | 58,676 |
| European (non-Finnish) | 0.00162% | 61,812 |
| South Asian | 0.00112% | 89,220 |
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.Val20=
- Coding
- c.60C>T
- MANE Select
- NM_006260
- dbSNP
- rs200556669
- Type
- single nucleotide variant
- Location
- chr13:95677315 (GRCh38)
- Gene constraint
- LOEUF 0.738 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.78 · 2 PDB
Similar variants
- DNAJC3 p.Arg393Ter Pathogenic/Likely pathogenic ★★ same type
- DNAJC3 p.Asp69Gly Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Leu231Val Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Ser450Cys Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Thr171Ile Uncertain significance ★★ ⚠ same type
- DNAJC3 c.848+10T>C Benign ★★ same type
- DNAJC3 p.Ala54= Benign/Likely benign ★★ same type
- DNAJC3 p.Gln99= Likely benign ★★ 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-val20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown