Is BUB1B p.Leu494Pro (c.1481T>C) pathogenic?

BUB1B p.Leu494Pro (c.1481T>C) is classified Uncertain significance in BUB1B (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-15). AlphaMissense: likely benign (0.0565); Absent from gnomAD v4.1.

How common is BUB1B p.Leu494Pro (c.1481T>C) in the general population?

BUB1B p.Leu494Pro (c.1481T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BUB1B p.Leu494Pro (c.1481T>C)?

AlphaMissense predicts likely benign (score 0.0565) — an in-silico prediction, not a clinical call.

BUB1B p.Leu494Pro

c.1481T>C · VCV4082864

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0565 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0565	likely benign
REVEL	0.014	strongly benign-leaning
SaProt	LLR -6.18	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.087	GERP -1.3
Regional constraint	o/e 0.91	unconstrained · MANE · 60 kb · p 0.0024 · regional, not allelic
Overall
CADD	12.23	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: BUB1B
Protein: p.Leu494Pro
Coding: c.1481T>C
MANE Select: NM_001211
Type: single nucleotide variant
Location: chr15:40200323 (GRCh38)
Gene constraint: LOEUF 0.707 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.62 · 9 PDB

Full BUB1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BUB1B p.Leu494= Likely benign ★★ same residue
BUB1B p.Arg114Ter Pathogenic ★★ same type
BUB1B p.Arg120Ter Pathogenic ★★ same type
BUB1B p.Arg194Ter Pathogenic/Likely pathogenic ★★ same type
BUB1B p.Arg199Ter Pathogenic/Likely pathogenic ★★ same type
BUB1B p.Arg67Ter Pathogenic/Likely pathogenic ★★ same type
BUB1B p.Gln267Ter Pathogenic ★★ same type
BUB1B p.Leu737Ter Pathogenic/Likely pathogenic ★★ 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/bub1b-p-leu494pro (accessed [today's date]).

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