Is DNAJB13 p.Pro33fs (c.98del) pathogenic?

DNAJB13 p.Pro33fs (c.98del) is classified Pathogenic in DNAJB13 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-08). Ultra-rare (popmax 0.0167%, amr).

How common is DNAJB13 p.Pro33fs (c.98del) in the general population?

DNAJB13 p.Pro33fs (c.98del) is ultra-rare (popmax 0.0167%, amr) (gnomAD).

DNAJB13 p.Pro33fs

c.98del · rs777186025 · VCV2076101

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0167%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1
Overall
CADD	23.7	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0167% Admixed American · 10/60,006 alleles

Filtering AF 0.009% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00681%

Overall 0.00062% 10/1,613,980 alleles · ultra-rare

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.Pro33fs
Coding: c.98del
MANE Select: NM_153614
dbSNP: rs777186025
Type: Deletion
Location: chr11:73958344 (GRCh38)
Gene constraint: LOEUF 0.9 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.81 · 1 PDB
Residue 33: the j domain

Full DNAJB13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJB13 p.Pro33= Likely benign ★ same residue
DNAJB13 p.Trp188fs Pathogenic ★ same type
DNAJB13 c.173-165del Likely benign ★ same type
DNAJB13 c.334+95_334+99del Benign ★ same type
DNAJB13 c.335-68_335-63del Likely benign ★ same type
DNAJB13 c.606+10del Benign ★ same type
DNAJB13 c.798-212_798-209del 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/dnajb13-p-pro33fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown