Is DNAJB9 p.Glu138Val (c.413A>T) pathogenic?

DNAJB9 p.Glu138Val (c.413A>T) is classified Uncertain significance in DNAJB9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-17). AlphaMissense: likely benign (0.2736); Absent from gnomAD v4.1.

How common is DNAJB9 p.Glu138Val (c.413A>T) in the general population?

DNAJB9 p.Glu138Val (c.413A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNAJB9 p.Glu138Val (c.413A>T)?

AlphaMissense predicts likely benign (score 0.2736) — an in-silico prediction, not a clinical call.

DNAJB9 p.Glu138Val

c.413A>T · VCV3841472

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2736 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2736	likely benign
REVEL	0.201	benign-leaning
SaProt	LLR -7.91	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.3	GERP 1.9, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 1,623 bp · p 0.5 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: DNAJB9
Protein: p.Glu138Val
Coding: c.413A>T
MANE Select: NM_012328
Type: single nucleotide variant
Location: chr7:108573094 (GRCh38)
Gene constraint: LOEUF 0.964 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.62 · 1 PDB
Residue 138: the 'divergent targeting domain' region

Full DNAJB9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJB9 p.Arg136His Benign ★★ same type
DNAJB9 p.Ala45Thr Uncertain significance ★ ⚠ same type
DNAJB9 p.Ala63Val Uncertain significance ★ ⚠ same type
DNAJB9 p.Ala80Asp Uncertain significance ★ ⚠ same type
DNAJB9 p.Arg101Gly Uncertain significance ★ ⚠ same type
DNAJB9 p.Arg144Cys Uncertain significance ★ ⚠ same type
DNAJB9 p.Arg82Gly Uncertain significance ★ ⚠ same type
DNAJB9 p.Asn81Asp 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/dnajb9-p-glu138val (accessed [today's date]).

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