Is DNAJC13 p.Arg895= (c.2685A>G) pathogenic?

DNAJC13 p.Arg895= (c.2685A>G) is classified Uncertain significance in DNAJC13 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-17). Very rare (popmax 0.00168%, amr); Associated with late-onset Parkinson disease.

What condition is associated with DNAJC13 p.Arg895= (c.2685A>G)?

DNAJC13 p.Arg895= (c.2685A>G) is associated with late-onset Parkinson disease (ClinVar).

How common is DNAJC13 p.Arg895= (c.2685A>G) in the general population?

DNAJC13 p.Arg895= (c.2685A>G) is very rare (popmax 0.00168%, amr) (gnomAD).

How is Hereditary late-onset Parkinson disease inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

DNAJC13 p.Arg895=

c.2685A>G · VCV4082096

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00168%, amr)

Conditions

late-onset Parkinson disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.69	donor gain · deltas
Pangolin	Δ0.73	gain · loss 0.41 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 9.2	GERP 1.9, phastCons 1
Overall
CADD	20.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00168% Admixed American · 1/59,580 alleles

Filtering AF 0.000803% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00065%

Overall 0.00118% 19/1,611,324 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00321%	31,186
Admixed Americangrpmax	0.00168%	59,580
European (non-Finnish)	0.00136%	73,702

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.Arg895=
Coding: c.2685A>G
MANE Select: NM_015268
Type: single nucleotide variant
Location: chr3:132478116 (GRCh38)
Gene constraint: LOEUF 0.267 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.91

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

Disease context

late-onset Parkinson disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary late-onset Parkinson disease (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

DNAJC13 p.Asn855Ser Conflicting classifications of pathogenicity ⚠ same condition
DNAJC13 p.Arg677Trp Uncertain significance ★★ ⚠ same type
DNAJC13 p.Arg833Lys Uncertain significance ★★ ⚠ same type
DNAJC13 p.Ile2055Leu Uncertain significance ★★ ⚠ same type
DNAJC13 p.Leu1834Val Uncertain significance ★★ ⚠ same type
DNAJC13 p.Met688Val Uncertain significance ★★ ⚠ same type
DNAJC13 p.Thr66Met Uncertain significance ★★ ⚠ same type
DNAJC13 c.1349+102C>T 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/dnajc13-p-arg895 (accessed [today's date]).

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