Is DNAJC7 p.Thr360Arg (c.1079C>G) pathogenic?

DNAJC7 p.Thr360Arg (c.1079C>G) is classified Uncertain significance in DNAJC7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-26). AlphaMissense: likely pathogenic (0.6435); Very rare (popmax 0.00134%, afr).

How common is DNAJC7 p.Thr360Arg (c.1079C>G) in the general population?

DNAJC7 p.Thr360Arg (c.1079C>G) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about DNAJC7 p.Thr360Arg (c.1079C>G)?

AlphaMissense predicts likely pathogenic (score 0.6435) — an in-silico prediction, not a clinical call.

DNAJC7 p.Thr360Arg

c.1079C>G · VCV3504047

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6435 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6435	likely pathogenic
REVEL	0.324	indeterminate
SaProt	LLR -10.83	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 0.64	unconstrained · MANE · 12 kb · p 9.4e-09 · regional, not allelic
Overall
CADD	27.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,630 alleles

Overall 0.000126% 2/1,587,422 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,630
European (non-Finnish)	8.58e-05%	1,165,414

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: DNAJC7
Protein: p.Thr360Arg
Coding: c.1079C>G
MANE Select: NM_003315
Type: single nucleotide variant
Location: chr17:41983568 (GRCh38)
Gene constraint: LOEUF 0.389 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.83

Full DNAJC7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJC7 c.167-65C>A Benign ★★ same type
DNAJC7 c.406-8C>T Benign ★★ same type
DNAJC7 c.599+161G>A Benign ★★ same type
DNAJC7 p.Pro193= Benign ★★ same type
DNAJC7 p.Ala115Pro Uncertain significance ★ ⚠ same type
DNAJC7 p.Ala141Thr Uncertain significance ★ ⚠ same type
DNAJC7 p.Ala370Val Uncertain significance ★ ⚠ same type
DNAJC7 p.Ala4Val 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/dnajc7-p-thr360arg (accessed [today's date]).

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