Is DNAJC13 p.Pro291= (c.873A>G) pathogenic?

DNAJC13 p.Pro291= (c.873A>G) is classified Likely benign in DNAJC13 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-18). Very rare (popmax 0.00939%, afr); Associated with DNAJC13-related disorder.

What condition is associated with DNAJC13 p.Pro291= (c.873A>G)?

DNAJC13 p.Pro291= (c.873A>G) is associated with DNAJC13-related disorder (ClinVar).

How common is DNAJC13 p.Pro291= (c.873A>G) in the general population?

DNAJC13 p.Pro291= (c.873A>G) is very rare (popmax 0.00939%, afr) (gnomAD).

DNAJC13 p.Pro291=

c.873A>G · rs372419664 · VCV3033667

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00939%, afr)

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 0.48	GERP -3.4, phastCons 0.8
Overall
CADD	8.678	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00939% African / African-American · 7/74,516 alleles

Filtering AF 0.00439% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0031%

Overall 0.000622% 10/1,608,688 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00939%	10,645
Admixed American	0.00506%	19,758

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.Pro291=
Coding: c.873A>G
MANE Select: NM_015268
dbSNP: rs372419664
Type: single nucleotide variant
Location: chr3:132454098 (GRCh38)
Gene constraint: LOEUF 0.267 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.91
Residue 291: 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-pro291 (accessed [today's date]).

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