Is PSMB4 p.Arg86= (c.258C>T) pathogenic?

PSMB4 p.Arg86= (c.258C>T) is classified Likely benign in PSMB4 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-19). Absent from gnomAD v4.1.

How common is PSMB4 p.Arg86= (c.258C>T) in the general population?

PSMB4 p.Arg86= (c.258C>T) is absent from gnomAD v4.1 (gnomAD).

PSMB4 p.Arg86=

c.258C>T · VCV3653850

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -3.6	GERP -4.6
Overall
CADD	10.1	PHRED · no single calibrated threshold — expert panels disagree

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: PSMB4
Protein: p.Arg86=
Coding: c.258C>T
MANE Select: NM_002796
Type: single nucleotide variant
Location: chr1:151400098 (GRCh38)
Gene constraint: LOEUF 0.659 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 87.70 · 150 PDB

Full PSMB4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PSMB4 c.-9G>A Uncertain significance ★★ same type
PSMB4 p.Ala17Ser Uncertain significance ★★ ⚠ same type
PSMB4 p.Arg211Cys Uncertain significance ★★ ⚠ same type
PSMB4 p.Asn230Asp Uncertain significance ★★ ⚠ same type
PSMB4 p.Asn230Ser Uncertain significance ★★ ⚠ same type
PSMB4 p.Asn83Ser Uncertain significance ★★ ⚠ same type
PSMB4 p.Asn92Lys Uncertain significance ★★ ⚠ same type
PSMB4 p.Asp212Tyr 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/psmb4-p-arg86 (accessed [today's date]).

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