DNAJC13 p.Pro2046=
c.6138G>A · VCV4533745
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0274%, 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 -0.3 | GERP -5.7, phastCons 0.001 |
| Overall | ||
| CADD | 4.407 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0274%
South Asian · 25/91,082 alleles
Filtering AF
0.019%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.00774%
125/1,614,164 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0274% | 3,643 |
| Finnishnot grpmax-eligible | 0.0125% | 8,004 |
| East Asian | 0.00891% | 11,220 |
| European (non-Finnish) | 0.00712% | 14,048 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
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
- DNAJC13
- Protein
- p.Pro2046=
- Coding
- c.6138G>A
- MANE Select
- NM_015268
- Type
- single nucleotide variant
- Location
- chr3:132525687 (GRCh38)
- Gene constraint
- LOEUF 0.267 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91
Similar variants
- DNAJC13 p.Pro2046Leu Uncertain significance ★ ⚠ same residue
- DNAJC13 p.Arg677Trp Uncertain significance ★★ ⚠ same type
- DNAJC13 p.Arg833Lys Uncertain significance ★★ ⚠ same type
- DNAJC13 p.Ile2055Leu Uncertain significance ★★ ⚠ same type
- DNAJC13 p.Leu1834Val Uncertain significance ★★ ⚠ same type
- DNAJC13 p.Met688Val Uncertain significance ★★ ⚠ same type
- DNAJC13 p.Thr66Met Uncertain significance ★★ ⚠ same type
- DNAJC13 c.1349+102C>T 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/dnajc13-p-pro2046 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown