Is DNAJB11 p.Arg34Ter (c.100C>T) pathogenic?

DNAJB11 p.Arg34Ter (c.100C>T) is classified Pathogenic in DNAJB11 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-30). Very rare (popmax 0.000425%, nfe); Associated with DNAJB11-related disorders.

What condition is associated with DNAJB11 p.Arg34Ter (c.100C>T)?

DNAJB11 p.Arg34Ter (c.100C>T) is associated with DNAJB11-related disorders, autosomal dominant polycystic kidney disease (ClinVar).

How common is DNAJB11 p.Arg34Ter (c.100C>T) in the general population?

DNAJB11 p.Arg34Ter (c.100C>T) is very rare (popmax 0.000425%, nfe) (gnomAD).

DNAJB11 p.Arg34Ter

c.100C>T · rs148976481 · VCV2053433

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000425%, nfe)

Conditions

DNAJB11-related disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 10
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2, phastCons 1
Overall
CADD	52.0	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 0.000425% European (non-Finnish) · 5/1,175,620 alleles

Filtering AF 0.000125% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.1e-05%

Overall 0.000345% 5/1,449,154 alleles · very 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: DNAJB11
Protein: p.Arg34Ter
Coding: c.100C>T
MANE Select: NM_016306
dbSNP: rs148976481
Type: single nucleotide variant
Location: chr3:186572126 (GRCh38)
Gene constraint: LOEUF 0.933 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.34
Residue 34: the j domain

Full DNAJB11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNAJB11-related disorders

Also linked: autosomal dominant polycystic kidney disease

Similar variants

DNAJB11 p.Arg34Gln Uncertain significance ★ ⚠ same residue
DNAJB11 p.Arg34Leu Uncertain significance ★ ⚠ same residue
DNAJB11 p.Arg206Ter Pathogenic ★★ same condition
DNAJB11 p.Arg242Ter Pathogenic ★★ same condition
DNAJB11 p.Arg24Ter Pathogenic ★★ same condition
DNAJB11 p.Glu144Ter Pathogenic/Likely pathogenic ★★ same condition
DNAJB11 p.Leu77Pro Likely pathogenic ★★ same condition
DNAJB11 p.Pro54Arg Likely pathogenic ★★ same condition

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-arg34ter (accessed [today's date]).

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