Is BUB1 p.Ile471= (c.1413C>T) pathogenic?

BUB1 p.Ile471= (c.1413C>T) is classified Likely benign in BUB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-08). Absent from gnomAD v4.1.

How common is BUB1 p.Ile471= (c.1413C>T) in the general population?

BUB1 p.Ile471= (c.1413C>T) is absent from gnomAD v4.1 (gnomAD).

BUB1 p.Ile471=

c.1413C>T · rs756814892 · VCV1772082

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/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.29	acceptor gain · deltas
Pangolin	Δ0.27	gain · loss 0.27 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 8.2	phastCons 1
Overall
CADD	17.94	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: BUB1
Protein: p.Ile471=
Coding: c.1413C>T
MANE Select: NM_004336
dbSNP: rs756814892
Type: single nucleotide variant
Location: chr2:110658513 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.91 · 11 PDB
Residue 471: an α-helix; the 'essential for loading of bubr1, mad1l1 and mad2l1 to kinetochores' region

Full BUB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BUB1 p.Ile471Leu Uncertain significance ★ ⚠ same residue
BUB1 p.Ile471Val Uncertain significance ★ ⚠ same residue
BUB1 c.1698+1G>T Uncertain significance ★★ same type
BUB1 p.Ala281Thr Uncertain significance ★★ ⚠ same type
BUB1 p.Ala283Thr Uncertain significance ★★ ⚠ same type
BUB1 p.Ala499Val Uncertain significance ★★ ⚠ same type
BUB1 p.Ala502Ser Uncertain significance ★★ ⚠ same type
BUB1 p.Ala630Gly 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/bub1-p-ile471 (accessed [today's date]).

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