Is DNAJC19 p.Tyr98His (c.292T>C) pathogenic?

DNAJC19 p.Tyr98His (c.292T>C) is classified Uncertain significance in DNAJC19 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-11). AlphaMissense: likely pathogenic (0.9881); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DNAJC19 p.Tyr98His (c.292T>C)?

DNAJC19 p.Tyr98His (c.292T>C) is associated with Inborn genetic diseases (ClinVar).

How common is DNAJC19 p.Tyr98His (c.292T>C) in the general population?

DNAJC19 p.Tyr98His (c.292T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNAJC19 p.Tyr98His (c.292T>C)?

AlphaMissense predicts likely pathogenic (score 0.9881) — an in-silico prediction, not a clinical call.

DNAJC19 p.Tyr98His

c.292T>C · VCV4617708

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9881 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9881	likely pathogenic
REVEL	0.437	indeterminate
SaProt	LLR -11.57	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 11	GERP 2, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 4,959 bp · p 0.0025 · regional, not allelic
Overall
CADD	28.9	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

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: DNAJC19
Protein: p.Tyr98His
Coding: c.292T>C
MANE Select: NM_145261
Type: single nucleotide variant
Location: chr3:180984699 (GRCh38)
Gene constraint: LOEUF 1.547 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.50
Residue 98: the j domain

Full DNAJC19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DNAJC19 p.Tyr98= Likely benign ★ same residue
DNAJC19 p.Ala25Thr Uncertain significance ★★ ⚠ same condition
DNAJC19 p.Arg20Cys Uncertain significance ★★ ⚠ same condition
DNAJC19 p.Arg84Gln Uncertain significance ★★ ⚠ same condition
DNAJC19 p.Gly68Ser Uncertain significance ★★ ⚠ same condition
DNAJC19 p.Ile66Met Uncertain significance ★★ ⚠ same condition
DNAJC19 p.Ile99Val Uncertain significance ★★ ⚠ same condition
DNAJC19 p.Val22Ile Uncertain significance ★★ ⚠ same condition

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/dnajc19-p-tyr98his (accessed [today's date]).

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