DNAJC12 p.Pro161=
c.483G>A · rs201470298 · VCV1542173
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0871%, eas)
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 -1.8 | GERP -4.4 |
| Overall | ||
| CADD | 5.137 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0871%
East Asian · 39/44,766 alleles
Filtering AF
0.0654%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0579%
Overall
0.00386%
62/1,608,182 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0871% | 1,148 |
| Remaining individualsnot grpmax-eligible | 0.00804% | 12,437 |
| South Asian | 0.00779% | 12,831 |
| Admixed American | 0.00171% | 58,322 |
| European (non-Finnish) | 0.000849% | 117,823 |
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
- DNAJC12
- Protein
- p.Pro161=
- Coding
- c.483G>A
- MANE Select
- NM_021800
- dbSNP
- rs201470298
- Type
- single nucleotide variant
- Location
- chr10:67805602 (GRCh38)
- Gene constraint
- LOEUF 1.193 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.84 · 1 PDB
- Residue 161
- a UniProt-annotated variant site (in hpanbh4; likely pathogenic); the 'disordered' region
Similar variants
- DNAJC12 p.Pro161Thr Uncertain significance ★ ⚠ same residue
- DNAJC12 p.Arg72Ter Pathogenic/Likely pathogenic ★★ same type
- DNAJC12 p.Gln162Ter Pathogenic/Likely pathogenic ★★ same type
- DNAJC12 p.Trp175Ter Pathogenic ★★ same type
- DNAJC12 p.Ala144Ser Uncertain significance ★★ ⚠ same type
- DNAJC12 p.Ala73Gly Uncertain significance ★★ ⚠ same type
- DNAJC12 p.Ala73Val Uncertain significance ★★ ⚠ same type
- DNAJC12 p.Arg180Cys 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/dnajc12-p-pro161 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown