Is DNAJC30 p.Leu201= (c.603C>T) pathogenic?

DNAJC30 p.Leu201= (c.603C>T) is classified Likely benign in DNAJC30 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-01). Very rare (popmax 0.000169%, nfe).

How common is DNAJC30 p.Leu201= (c.603C>T) in the general population?

DNAJC30 p.Leu201= (c.603C>T) is very rare (popmax 0.000169%, nfe) (gnomAD).

DNAJC30 p.Leu201=

c.603C>T · rs2484462747 · VCV2657564

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

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 1.5	GERP 0.11, phastCons 0.92
Overall
CADD	4.78	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000169% European (non-Finnish) · 2/1,180,028 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000137% 2/1,461,774 alleles · very rare

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: DNAJC30
Protein: p.Leu201=
Coding: c.603C>T
MANE Select: NM_032317
dbSNP: rs2484462747
Type: single nucleotide variant
Location: chr7:73682821 (GRCh38)
Gene constraint: LOEUF 1.484 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.87 · 1 PDB

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-leu201 (accessed [today's date]).

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