Is DNAJC13 p.Arg1069Gln (c.3206G>A) pathogenic?

DNAJC13 p.Arg1069Gln (c.3206G>A) is classified Uncertain significance in DNAJC13 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-28). AlphaMissense: likely pathogenic (0.7913); Very rare (popmax 0.0011%, sas).

How common is DNAJC13 p.Arg1069Gln (c.3206G>A) in the general population?

DNAJC13 p.Arg1069Gln (c.3206G>A) is very rare (popmax 0.0011%, sas) (gnomAD).

What do computational predictors say about DNAJC13 p.Arg1069Gln (c.3206G>A)?

AlphaMissense predicts likely pathogenic (score 0.7913) — an in-silico prediction, not a clinical call.

DNAJC13 p.Arg1069Gln

c.3206G>A · rs1482268756 · VCV2480666

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7913 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7913	likely pathogenic
REVEL	0.385	indeterminate
SaProt	LLR -7.25	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.1, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 60 kb · p 1.2e-06 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,078 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000274% 4/1,461,774 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,078
European (non-Finnish)	0.000254%	393,318

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.Arg1069Gln
Coding: c.3206G>A
MANE Select: NM_015268
dbSNP: rs1482268756
Type: single nucleotide variant
Location: chr3:132484611 (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

Similar variants

DNAJC13 p.Arg1069Trp Uncertain significance ★ ⚠ same residue
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-arg1069gln (accessed [today's date]).

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