DNAJC13 p.Arg912=
c.2736G>A · rs61748099 · VCV769279
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.467%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.29 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.42 | GERP -3.8, phastCons 0.85 |
| Overall | ||
| CADD | 11.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.467%
European (non-Finnish) · 5,488/1,175,514 alleles
Filtering AF
0.457%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.452%
Overall
0.369%
5,939/1,608,368 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.467% | 214 |
| Remaining individualsnot grpmax-eligible | 0.434% | 231 |
| Finnishnot grpmax-eligible | 0.132% | 760 |
| African / African-American | 0.0814% | 1,228 |
| Admixed American | 0.0501% | 1,995 |
| Middle Eastern | 0.0166% | 6,038 |
| South Asian | 0.0044% | 22,715 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,524 |
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.Arg912=
- Coding
- c.2736G>A
- MANE Select
- NM_015268
- dbSNP
- rs61748099
- Type
- single nucleotide variant
- Location
- chr3:132479253 (GRCh38)
- Gene constraint
- LOEUF 0.267 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91
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-arg912 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown