Is BUB1 p.His1024fs (c.3069del) pathogenic?

BUB1 p.His1024fs (c.3069del) is classified Pathogenic in BUB1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 1998-03-19). Absent from gnomAD; Associated with colon carcinoma.

What condition is associated with BUB1 p.His1024fs (c.3069del)?

BUB1 p.His1024fs (c.3069del) is associated with colon carcinoma (ClinVar).

How common is BUB1 p.His1024fs (c.3069del) in the general population?

BUB1 p.His1024fs (c.3069del) is absent from gnomAD (gnomAD).

BUB1 p.His1024fs

c.3069del · rs587776642 · VCV6759

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

colon carcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (25 of 25) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.2	phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BUB1
Protein: p.His1024fs
Coding: c.3069del
MANE Select: NM_004336
dbSNP: rs587776642
Type: Deletion
Location: chr2:110638153 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.91 · 11 PDB
Residue 1024: the protein kinase domain

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

Disease context

colon carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BUB1 p.His1024Arg Uncertain significance ★★ ⚠ same residue
BUB1 p.His1024Leu Uncertain significance ★ ⚠ same residue
BUB1 p.Gln170fs Uncertain significance ★ same type
BUB1 p.Gln503fs Uncertain significance ★ same type
BUB1 p.Lys1053fs Uncertain significance ★ same type
BUB1 c.1699-20del Likely benign ★ same type
BUB1 c.567+7del Likely benign ★ same type
BUB1 c.958-15del Likely benign ★ 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-his1024fs (accessed [today's date]).

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