DNAJB13 p.Ser7=
c.21T>G · rs752063049 · VCV1899802
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
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 -1.8 | GERP -4.2 |
| Overall | ||
| CADD | 5.275 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,002 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00112%
18/1,614,010 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,572 |
| African / African-American | 0.00801% | 12,489 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
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
- DNAJB13
- Protein
- p.Ser7=
- Coding
- c.21T>G
- MANE Select
- NM_153614
- dbSNP
- rs752063049
- Type
- single nucleotide variant
- Location
- chr11:73951090 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.81 · 1 PDB
- Residue 7
- the j domain
Similar variants
- DNAJB13 p.Ser7Thr Conflicting classifications of pathogenicity ★ same residue
- DNAJB13 p.Gln136Ter Pathogenic/Likely pathogenic ★★ same type
- DNAJB13 p.Arg131Gln Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Arg142Gln Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Arg222Cys Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Arg301Cys Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Asn14Asp Uncertain significance ★★ ⚠ same type
- DNAJB13 p.Asp169Gly 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/dnajb13-p-ser7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown