Is DNAJC13 p.Val1783= (c.5349T>C) pathogenic?

DNAJC13 p.Val1783= (c.5349T>C) is classified Likely benign in DNAJC13 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-16). Very rare (popmax 0.0067%, nfe); Associated with DNAJC13-related disorder.

What condition is associated with DNAJC13 p.Val1783= (c.5349T>C)?

DNAJC13 p.Val1783= (c.5349T>C) is associated with DNAJC13-related disorder (ClinVar).

How common is DNAJC13 p.Val1783= (c.5349T>C) in the general population?

DNAJC13 p.Val1783= (c.5349T>C) is very rare (popmax 0.0067%, nfe) (gnomAD).

DNAJC13 p.Val1783=

c.5349T>C · rs757020974 · VCV3050646

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0067%, 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 -0.093	GERP 0.073, phastCons 0.54
Overall
CADD	6.473	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0067% European (non-Finnish) · 79/1,179,492 alleles

Filtering AF 0.00547% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00506%

Overall 0.00496% 80/1,613,304 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0067%	14,930
Remaining individualsnot grpmax-eligible	0.0016%	62,444

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.Val1783=
Coding: c.5349T>C
MANE Select: NM_015268
dbSNP: rs757020974
Type: single nucleotide variant
Location: chr3:132513063 (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

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-val1783 (accessed [today's date]).

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