DNAJB11 p.Asn353=
c.1059T>C · rs140521819 · VCV2712697
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.088%, 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 0.32 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 6.782 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.088%
African / African-American · 66/74,986 alleles
Filtering AF
0.0709%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0648%
Overall
0.00441%
71/1,610,986 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.088% | 1,136 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,471 |
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
- DNAJB11
- Protein
- p.Asn353=
- Coding
- c.1059T>C
- MANE Select
- NM_016306
- dbSNP
- rs140521819
- Type
- single nucleotide variant
- Location
- chr3:186585390 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.34
- Residue 353
- a UniProt-annotated variant site (in pkd6)
Similar variants
- DNAJB11 p.Arg206Ter Pathogenic ★★ same type
- DNAJB11 p.Arg242Ter Pathogenic ★★ same type
- DNAJB11 p.Arg24Ter Pathogenic ★★ same type
- DNAJB11 p.Arg34Ter Pathogenic ★★ same type
- DNAJB11 p.Glu144Ter Pathogenic/Likely pathogenic ★★ same type
- DNAJB11 p.Leu77Pro Likely pathogenic ★★ same type
- DNAJB11 p.Pro54Arg Likely pathogenic ★★ same type
- DNAJB11 p.Ala297Val 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/dnajb11-p-asn353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown