DNAJC17 p.Lys88=
c.264A>G · rs754531539 · VCV1644388
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00525%, 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 -0.41 | GERP -3.4, phastCons 0.2 |
| Overall | ||
| CADD | 8.298 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00525%
European (non-Finnish) · 62/1,180,016 alleles
Filtering AF
0.00418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.0039%
63/1,613,946 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00525% | 19,033 |
| African / African-American | 0.00134% | 74,876 |
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.Lys88=
- Coding
- c.264A>G
- MANE Select
- NM_018163
- dbSNP
- rs754531539
- Type
- single nucleotide variant
- Location
- chr15:40779254 (GRCh38)
- Gene constraint
- LOEUF 0.95 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.72 · 1 PDB
- Residue 88
- the 'disordered' region
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-lys88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown