DNAJB13 p.Tyr52=
c.156C>T · rs146073659 · VCV1569493
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0748%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.9 | GERP -4.2 |
| Overall | ||
| CADD | 2.735 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0748%
European (non-Finnish) · 883/1,180,002 alleles
Filtering AF
0.0707%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.069%
Overall
0.0596%
962/1,614,144 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0748% | 1,336 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,786 |
| Admixed American | 0.0367% | 2,728 |
| Finnishnot grpmax-eligible | 0.0187% | 5,335 |
| African / African-American | 0.0133% | 7,504 |
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
- DNAJB13
- Protein
- p.Tyr52=
- Coding
- c.156C>T
- MANE Select
- NM_153614
- dbSNP
- rs146073659
- Type
- single nucleotide variant
- Location
- chr11:73958404 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.81 · 1 PDB
- Residue 52
- the j domain
Similar variants
- DNAJB13 p.Gln136Ter Pathogenic/Likely pathogenic ★★ same type
- DNAJB13 p.Arg131Gln Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Arg142Gln Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Arg222Cys Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Arg301Cys Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Asn14Asp Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Asp169Gly Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Asp65Asn 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/dnajb13-p-tyr52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown