Is DNAJC13 p.Arg360= (c.1080G>A) pathogenic?

DNAJC13 p.Arg360= (c.1080G>A) is classified Likely benign in DNAJC13 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-27). Ultra-rare (popmax 0.0135%, nfe); Associated with DNAJC13-related disorder.

What condition is associated with DNAJC13 p.Arg360= (c.1080G>A)?

DNAJC13 p.Arg360= (c.1080G>A) is associated with DNAJC13-related disorder (ClinVar).

How common is DNAJC13 p.Arg360= (c.1080G>A) in the general population?

DNAJC13 p.Arg360= (c.1080G>A) is ultra-rare (popmax 0.0135%, nfe) (gnomAD).

DNAJC13 p.Arg360=

c.1080G>A · rs369628764 · VCV3052589

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0135%, nfe)

Conditions

DNAJC13-related disorder

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	GERP -3.4, phastCons 1
Overall
CADD	7.17	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0135% European (non-Finnish) · 159/1,179,670 alleles

Filtering AF 0.0117% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0111%

Overall 0.0105% 170/1,613,054 alleles · ultra-rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0144%	6,936
European (non-Finnish)grpmax	0.0135%	7,419
Admixed American	0.00334%	29,905

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Arg360=
Coding: c.1080G>A
MANE Select: NM_015268
dbSNP: rs369628764
Type: single nucleotide variant
Location: chr3:132456382 (GRCh38)
Gene constraint: LOEUF 0.267 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.91
Residue 360: the 'involved in membrane association' region

Full DNAJC13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNAJC13-related disorder

Similar variants

DNAJC13 p.Ile2055Leu Uncertain significance ★★ ⚠ same condition
DNAJC13 p.Thr66Met Uncertain significance ★★ ⚠ same condition
DNAJC13 p.His33Arg Uncertain significance ★ ⚠ same condition
DNAJC13 p.Ile1691Val Uncertain significance ★ ⚠ same condition
DNAJC13 p.Ala1839Val Uncertain significance same condition
DNAJC13 p.Ala183Val Uncertain significance ⚠ same condition
DNAJC13 p.Cys1083Ser Uncertain significance ⚠ same condition
DNAJC13 p.Val1995Ile Uncertain significance ⚠ 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/dnajc13-p-arg360 (accessed [today's date]).

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