DNAJC5 p.Leu20=
c.60T>C · rs745419250 · VCV1640594
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000678%, nfe)
Conditions
1
neuronal ceroid lipofuscinosis
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 -3.5 | GERP -5 |
| Overall | ||
| CADD | 0.736 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000678%
European (non-Finnish) · 8/1,180,046 alleles
Filtering AF
0.000292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.000496%
8/1,613,980 alleles · very rare
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.Leu20=
- Coding
- c.60T>C
- MANE Select
- NM_025219
- dbSNP
- rs745419250
- Type
- single nucleotide variant
- Location
- chr20:63928405 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.09 · 2 PDB
- Residue 20
- the j domain; an α-helix
Similar variants
- DNAJC5 p.Leu20Phe Uncertain significance ★★ ⚠ same residue
- DNAJC5 p.Ala176Val Uncertain significance ★★ ⚠ same condition
- DNAJC5 p.Ala26Thr Uncertain significance ★★ ⚠ same condition
- DNAJC5 p.Ala54Thr Uncertain significance ★★ ⚠ same condition
- DNAJC5 p.Ala54Val Uncertain significance ★★ ⚠ same condition
- DNAJC5 p.Ala63Thr Uncertain significance ★★ ⚠ same condition
- DNAJC5 p.Arg164Lys Uncertain significance ★★ ⚠ same condition
- DNAJC5 p.Arg36Gln Uncertain significance ★★ ⚠ same condition
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-leu20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown