DNAJC12 p.Ser26=
c.78G>A · rs1409943805 · VCV1370239
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000775%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | donor loss at this position · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.71 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 24.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000775%
European (non-Finnish) · 9/1,160,726 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000264%
Overall
0.000567%
9/1,586,206 alleles · very rare
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.Ser26=
- Coding
- c.78G>A
- MANE Select
- NM_021800
- dbSNP
- rs1409943805
- Type
- single nucleotide variant
- Location
- chr10:67837934 (GRCh38)
- Gene constraint
- LOEUF 1.193 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.84 · 1 PDB
- Residue 26
- the j domain
Similar variants
- DNAJC12 p.Ser26Leu 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-ser26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown