DNAJB2 p.Asp33=
c.99C>T · VCV4852984
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 4 | GERP 0.2, phastCons 1 |
| Overall | ||
| CADD | 14.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/59,980 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000274%
4/1,461,840 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 29,990 |
| European (non-Finnish) | 0.000169% | 590,005 |
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
- DNAJB2
- Protein
- p.Asp33=
- Coding
- c.99C>T
- MANE Select
- NM_006736
- Type
- single nucleotide variant
- Location
- chr2:219280611 (GRCh38)
- Gene constraint
- LOEUF 0.836 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.73 · 1 PDB
- Residue 33
- the j domain; a turn
Similar variants
- DNAJB2 p.Asp33Glu Uncertain significance ★ ⚠ same residue
- DNAJB2 c.175+2T>A Pathogenic/Likely pathogenic ★★ same type
- DNAJB2 c.352+1G>A Pathogenic ★★ same type
- DNAJB2 c.65+1G>A Likely pathogenic ★★ same type
- DNAJB2 p.Arg104Gln Uncertain significance ★★ ⚠ same type
- DNAJB2 p.Arg165Cys Uncertain significance ★★ ⚠ same type
- DNAJB2 p.Arg178His Uncertain significance ★★ ⚠ same type
- DNAJB2 p.Arg182Cys 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/dnajb2-p-asp33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown