Is BUB1 p.Thr3= (c.9C>G) pathogenic?

BUB1 p.Thr3= (c.9C>G) is classified Likely benign in BUB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-03-16). Very rare (popmax 0.00448%, eas).

How common is BUB1 p.Thr3= (c.9C>G) in the general population?

BUB1 p.Thr3= (c.9C>G) is very rare (popmax 0.00448%, eas) (gnomAD).

BUB1 p.Thr3=

c.9C>G · rs1289597246 · VCV1768915

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00448%, eas)

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 2.3	phastCons 0.99
Overall
CADD	8.447	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00448% East Asian · 2/44,642 alleles

Filtering AF 0.000743% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000278%

Overall 0.000137% 2/1,456,542 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.Thr3=
Coding: c.9C>G
MANE Select: NM_004336
dbSNP: rs1289597246
Type: single nucleotide variant
Location: chr2:110677987 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.91 · 11 PDB
Residue 3: the 'necessary for kinetochore localization' region; an α-helix

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

Similar variants

BUB1 p.Thr3Ile Uncertain significance ★★ ⚠ same residue
BUB1 p.Thr3Ala Uncertain significance ★ ⚠ same residue
BUB1 p.Thr3Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
BUB1 p.Thr3Pro 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

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-thr3 (accessed [today's date]).

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