Is DNAJC16 p.Val154Phe (c.460G>T) pathogenic?

DNAJC16 p.Val154Phe (c.460G>T) is classified Uncertain significance in DNAJC16 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-03). AlphaMissense: likely benign (0.2376); Ultra-rare (popmax 0.0165%, mid).

How common is DNAJC16 p.Val154Phe (c.460G>T) in the general population?

DNAJC16 p.Val154Phe (c.460G>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about DNAJC16 p.Val154Phe (c.460G>T)?

AlphaMissense predicts likely benign (score 0.2376) — an in-silico prediction, not a clinical call.

DNAJC16 p.Val154Phe

c.460G>T · VCV3503981

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2376 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2376	likely benign
REVEL	0.151	moderately benign-leaning
SaProt	LLR -6.20	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 7.4	GERP 0.62, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 39 kb · p 0.017 · regional, not allelic
Overall
CADD	25.6	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

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Overall 6.2e-05% 1/1,614,158 alleles · ultra-rare exomes 1/1,461,894 · genomes 0/152,264 · joint denominator

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: DNAJC16
Protein: p.Val154Phe
Coding: c.460G>T
MANE Select: NM_015291
Type: single nucleotide variant
Location: chr1:15536700 (GRCh38)
Gene constraint: LOEUF 0.933 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.54
Residue 154: the thioredoxin domain

Full DNAJC16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAJC16 p.Ala337Gly Uncertain significance ★ ⚠ same type
DNAJC16 p.Ala53Ser Uncertain significance ★ ⚠ same type
DNAJC16 p.Ala53Thr Uncertain significance ★ ⚠ same type
DNAJC16 p.Ala95Thr Uncertain significance ★ ⚠ same type
DNAJC16 p.Arg111His Uncertain significance ★ ⚠ same type
DNAJC16 p.Arg113His Uncertain significance ★ ⚠ same type
DNAJC16 p.Arg134Gln Uncertain significance ★ ⚠ same type
DNAJC16 p.Arg204Lys 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/dnajc16-p-val154phe (accessed [today's date]).

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