Is DNAJC30 p.Val99= (c.297G>A) pathogenic?

DNAJC30 p.Val99= (c.297G>A) is classified Likely benign in DNAJC30 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-01). Absent from gnomAD v4.1.

How common is DNAJC30 p.Val99= (c.297G>A) in the general population?

DNAJC30 p.Val99= (c.297G>A) is absent from gnomAD v4.1 (gnomAD).

DNAJC30 p.Val99=

c.297G>A · VCV4823496

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.78	GERP 3.9, phastCons 1
Overall
CADD	13.27	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DNAJC30
Protein: p.Val99=
Coding: c.297G>A
MANE Select: NM_032317
Type: single nucleotide variant
Location: chr7:73683127 (GRCh38)
Gene constraint: LOEUF 1.484 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.87 · 1 PDB
Residue 99: an α-helix; the j domain

Full DNAJC30 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJC30 p.Tyr51Cys Pathogenic/Likely pathogenic ★★ same type
DNAJC30 p.Gly34Arg Benign ★★ same type
DNAJC30 p.Trp8Ter Likely pathogenic ★ same type
DNAJC30 p.Tyr98Ser Likely pathogenic ★ same type
DNAJC30 c.*122C>T Uncertain significance ★ same type
DNAJC30 p.Ala153Ser Uncertain significance ★ ⚠ same type
DNAJC30 p.Ala157Val Uncertain significance ★ ⚠ same type
DNAJC30 p.Ala20Val Uncertain significance ★ ⚠ 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/dnajc30-p-val99 (accessed [today's date]).

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