DNAJC3 p.Tyr26=
c.78C>T · rs146543814 · VCV710813
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.81%, sas)
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 1.6 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 15.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.81%
South Asian · 1,616/89,136 alleles
Filtering AF
1.74%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.71%
Overall
0.34%
5,430/1,598,302 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.81% | 55 |
| Middle Eastern | 1.33% | 75 |
| Remaining individualsnot grpmax-eligible | 0.412% | 243 |
| Admixed American | 0.292% | 343 |
| European (non-Finnish) | 0.275% | 364 |
| Ashkenazi Jewishnot grpmax-eligible | 0.138% | 726 |
| African / African-American | 0.0317% | 3,153 |
| Finnishnot grpmax-eligible | 0.0236% | 4,246 |
| East Asian | 0.00234% | 42,686 |
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
- DNAJC3
- Protein
- p.Tyr26=
- Coding
- c.78C>T
- MANE Select
- NM_006260
- dbSNP
- rs146543814
- Type
- single nucleotide variant
- Location
- chr13:95677333 (GRCh38)
- Gene constraint
- LOEUF 0.738 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.78 · 2 PDB
Similar variants
- DNAJC3 p.Arg393Ter Pathogenic/Likely pathogenic ★★ same type
- DNAJC3 p.Asp69Gly Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Leu231Val Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Ser450Cys Uncertain significance ★★ ⚠ same type
- DNAJC3 p.Thr171Ile Uncertain significance ★★ ⚠ same type
- DNAJC3 c.848+10T>C Benign ★★ same type
- DNAJC3 p.Ala54= Benign/Likely benign ★★ same type
- DNAJC3 p.Gln99= Likely benign ★★ 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/dnajc3-p-tyr26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown