DNAJC17 p.Pro40=
c.120A>T · rs1360556449 · VCV1915050
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 -0.68 | GERP 0.81, phastCons 0.048 |
| Overall | ||
| CADD | 10.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,010 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000434%
7/1,614,082 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,003 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
| African / African-American | 0.00267% | 37,466 |
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
- DNAJC17
- Protein
- p.Pro40=
- Coding
- c.120A>T
- MANE Select
- NM_018163
- dbSNP
- rs1360556449
- Type
- single nucleotide variant
- Location
- chr15:40779956 (GRCh38)
- Gene constraint
- LOEUF 0.95 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.72 · 1 PDB
- Residue 40
- the j domain
Similar variants
- DNAJC17 p.Ala227= Uncertain significance ★★ same type
- DNAJC17 p.Ala23Glu Uncertain significance ★★ ⚠ same type
- DNAJC17 p.Ala35Thr Uncertain significance ★★ ⚠ same type
- DNAJC17 p.Arg103Trp Uncertain significance ★★ ⚠ same type
- DNAJC17 p.Arg105Trp Uncertain significance ★★ ⚠ same type
- DNAJC17 p.Arg119Trp Uncertain significance ★★ ⚠ same type
- DNAJC17 p.Arg151Cys Uncertain significance ★★ ⚠ same type
- DNAJC17 p.Arg151Leu 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/dnajc17-p-pro40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown