DNAJC5 p.Arg7=
c.21C>T · rs1227078334 · VCV3250893
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00271%, nfe)
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 0.32 | GERP -2.6, phastCons 0.99 |
| Overall | ||
| CADD | 8.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00271%
European (non-Finnish) · 32/1,179,770 alleles
Filtering AF
0.00196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00168%
Overall
0.00205%
33/1,613,644 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00271% | 36,868 |
| African / African-American | 0.00133% | 74,934 |
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
- DNAJC5
- Protein
- p.Arg7=
- Coding
- c.21C>T
- MANE Select
- NM_025219
- dbSNP
- rs1227078334
- Type
- single nucleotide variant
- Location
- chr20:63928366 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.09 · 2 PDB
- Residue 7
- an α-helix
Similar variants
- DNAJC5 p.Arg7Cys Uncertain significance ★ ⚠ same residue
- DNAJC5 p.Arg7His Uncertain significance ★ ⚠ same residue
- DNAJC5 p.Leu115Arg Pathogenic ★★ same type
- DNAJC5 c.-109A>G Uncertain significance ★★ same type
- DNAJC5 c.-11-2A>G Uncertain significance ★★ same type
- DNAJC5 p.Ala176Val Uncertain significance ★★ ⚠ same type
- DNAJC5 p.Ala26Thr Uncertain significance ★★ ⚠ same type
- DNAJC5 p.Ala54Thr 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/dnajc5-p-arg7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown