DNAJC3 p.Ala54=
c.162T>G · rs61758425 · VCV724566
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.176%, 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 -0.7 | phastCons 0.021 |
| Overall | ||
| CADD | 7.605 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.176%
European (non-Finnish) · 2,064/1,169,452 alleles
Filtering AF
0.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.168%
Overall
0.141%
2,246/1,590,026 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.176% | 567 |
| Remaining individualsnot grpmax-eligible | 0.124% | 807 |
| Finnishnot grpmax-eligible | 0.0756% | 1,323 |
| Admixed American | 0.039% | 2,567 |
| Middle Eastern | 0.0333% | 3,000 |
| South Asian | 0.0268% | 3,731 |
| African / African-American | 0.0135% | 7,410 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00342% | 29,238 |
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.Ala54=
- Coding
- c.162T>G
- MANE Select
- NM_006260
- dbSNP
- rs61758425
- Type
- single nucleotide variant
- Location
- chr13:95709306 (GRCh38)
- Gene constraint
- LOEUF 0.738 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.78 · 2 PDB
- Residue 54
- an α-helix
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.Gln99= Likely benign ★★ same type
- DNAJC3 p.Glu354Gln Benign/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-ala54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown