DNAJC13 p.Pro1314=
c.3942G>A · rs35658317 · VCV709668
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.65%, afr)
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 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 12.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.65%
African / African-American · 1,238/74,936 alleles
Filtering AF
1.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.54%
Overall
0.0994%
1,603/1,612,414 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.65% | 61 |
| Ashkenazi Jewishnot grpmax-eligible | 0.348% | 287 |
| Remaining individualsnot grpmax-eligible | 0.175% | 573 |
| Middle Eastern | 0.116% | 866 |
| Admixed American | 0.108% | 922 |
| European (non-Finnish) | 0.00645% | 15,511 |
| South Asian | 0.0044% | 22,726 |
| Finnishnot grpmax-eligible | 0.00156% | 63,990 |
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.Pro1314=
- Coding
- c.3942G>A
- MANE Select
- NM_015268
- dbSNP
- rs35658317
- Type
- single nucleotide variant
- Location
- chr3:132495088 (GRCh38)
- Gene constraint
- LOEUF 0.267 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91
- Residue 1314
- the j domain
Similar variants
- 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
- DNAJC13 c.1349+103C>A 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-pro1314 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown