DNAJC12 p.Ser81=
c.243C>T · rs3740049 · VCV1169625
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 30.7%, eas) — too common for a highly-penetrant pathogenic allele
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 3 | GERP -0.54, phastCons 1 |
| Overall | ||
| CADD | 12.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
30.7%
East Asian · 13,795/44,862 alleles
Filtering AF
30.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 30.1%
Overall
11.1%
178,968/1,613,968 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 30.7% | 3 |
| Admixed American | 17.8% | 6 |
| Finnishnot grpmax-eligible | 17.6% | 6 |
| Amishnot grpmax-eligible | 15.5% | 6 |
| South Asian | 13% | 8 |
| Remaining individualsnot grpmax-eligible | 10.9% | 9 |
| European (non-Finnish) | 10.1% | 10 |
| Middle Eastern | 9.98% | 10 |
| Ashkenazi Jewishnot grpmax-eligible | 5.01% | 20 |
| African / African-American | 3.52% | 28 |
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.Ser81=
- Coding
- c.243C>T
- MANE Select
- NM_021800
- dbSNP
- rs3740049
- Type
- single nucleotide variant
- Location
- chr10:67811578 (GRCh38)
- Gene constraint
- LOEUF 1.193 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.84 · 1 PDB
- Residue 81
- a UniProt-annotated variant site (in hpanbh4; likely pathogenic); an α-helix
Similar variants
- 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
- DNAJC12 p.Arg180His 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-ser81 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown