Is DNAJC17 p.Cys38= (c.114C>T) pathogenic?

DNAJC17 p.Cys38= (c.114C>T) is classified Likely benign in DNAJC17 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-23). Very rare (popmax 0.00223%, eas).

How common is DNAJC17 p.Cys38= (c.114C>T) in the general population?

DNAJC17 p.Cys38= (c.114C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

DNAJC17 p.Cys38=

c.114C>T · VCV4708390

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

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 2.2	GERP -0.36, phastCons 1
Overall
CADD	9.716	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,886 alleles

Overall 6.84e-05% 1/1,461,796 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: DNAJC17
Protein: p.Cys38=
Coding: c.114C>T
MANE Select: NM_018163
Type: single nucleotide variant
Location: chr15:40779962 (GRCh38)
Gene constraint: LOEUF 0.95 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.72 · 1 PDB
Residue 38: the j domain

Full DNAJC17 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GCHFR p.Arg38Gly Uncertain significance ★ ⚠ same residue
DNAJC17 p.Ala227= Uncertain significance ★★ same type
DNAJC17 p.Ala23Glu Uncertain significance ★★ ⚠ same type
DNAJC17 p.Ala35Thr Uncertain significance ★★ ⚠ same type
DNAJC17 p.Arg103Trp Uncertain significance ★★ ⚠ same type
DNAJC17 p.Arg105Trp Uncertain significance ★★ ⚠ same type
DNAJC17 p.Arg119Trp Uncertain significance ★★ ⚠ same type
DNAJC17 p.Arg151Cys 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/dnajc17-p-cys38 (accessed [today's date]).

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