Is BUB1 p.Arg1082Ser (c.3244C>A) pathogenic?

BUB1 p.Arg1082Ser (c.3244C>A) is classified Uncertain significance in BUB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-31). AlphaMissense: likely pathogenic (0.5923); Very rare (popmax 0.00138%, sas).

How common is BUB1 p.Arg1082Ser (c.3244C>A) in the general population?

BUB1 p.Arg1082Ser (c.3244C>A) is very rare (popmax 0.00138%, sas) (gnomAD).

What do computational predictors say about BUB1 p.Arg1082Ser (c.3244C>A)?

AlphaMissense predicts likely pathogenic (score 0.5923) — an in-silico prediction, not a clinical call.

BUB1 p.Arg1082Ser

c.3244C>A · rs372788700 · VCV2565819

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5923 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00138%, sas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.5923	likely pathogenic
REVEL	0.214	benign-leaning
SaProt	LLR -5.98	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 40 kb · p 0.00043 · regional, not allelic
Overall
CADD	23.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00138% South Asian · 1/72,240 alleles

Overall 7.44e-05% 1/1,344,506 alleles · very rare

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: BUB1
Protein: p.Arg1082Ser
Coding: c.3244C>A
MANE Select: NM_004336
dbSNP: rs372788700
Type: single nucleotide variant
Location: chr2:110637978 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.91 · 11 PDB
Residue 1082: the protein kinase domain

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

Similar variants

BUB1 p.Arg1082Cys Uncertain significance ★★ ⚠ same residue
BUB1 p.Arg1082Gly Uncertain significance ★ ⚠ same residue
BUB1 p.Arg1082His Uncertain significance ★ ⚠ same residue
BUB1 p.Arg1082= Likely benign ★ 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

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-arg1082ser (accessed [today's date]).

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