Is DNAJC5 p.Thr167= (c.501A>G) pathogenic?

DNAJC5 p.Thr167= (c.501A>G) is classified Benign in DNAJC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-01-28). Absent from gnomAD v4.1.

How common is DNAJC5 p.Thr167= (c.501A>G) in the general population?

DNAJC5 p.Thr167= (c.501A>G) is absent from gnomAD v4.1 (gnomAD).

DNAJC5 p.Thr167=

c.501A>G · rs587780922 · VCV137125

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,560,608)

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 1.4	GERP -0.51, phastCons 1
Overall
CADD	14.68	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,560,608). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DNAJC5
Protein: p.Thr167=
Coding: c.501A>G
MANE Select: NM_025219
dbSNP: rs587780922
Type: single nucleotide variant
Location: chr20:63931472 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.09 · 2 PDB

Full DNAJC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJC5 p.Thr167Ile Uncertain significance ★ ⚠ same residue
DNAJC5 p.Leu115Arg Pathogenic ★★ same type
DNAJC5 c.-109A>G Uncertain significance ★★ same type
DNAJC5 c.-11-2A>G Uncertain significance ★★ same type
DNAJC5 p.Ala176Val Uncertain significance ★★ ⚠ same type
DNAJC5 p.Ala26Thr Uncertain significance ★★ ⚠ same type
DNAJC5 p.Ala54Thr Uncertain significance ★★ ⚠ same type
DNAJC5 p.Ala54Val 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/dnajc5-p-thr167 (accessed [today's date]).

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