# NM_004336.5(BUB1):c.3069del (p.His1024fs)

https://sugi.bio/variant/bub1-p-his1024fs

## Summary

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

**At a glance:** Pathogenic · review: No assertion criteria · rsID rs587776642 · 1 submitter · 1 linked condition · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the BUB1 gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, and is linked to colon carcinoma.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Clinical trials | 1091 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [BUB1](https://sugi.bio/atlas/gene/BUB1/) |
| Protein change (HGVS p.) | p.His1024fs |
| Coding change (HGVS c.) | c.3069del |
| MANE Select transcript | [NM_004336](https://www.ncbi.nlm.nih.gov/nuccore/NM_004336) |
| dbSNP | [rs587776642](https://www.ncbi.nlm.nih.gov/snp/rs587776642/) |
| Variant type | Deletion |
| Location | chr2:110638153-110638153 (GRCh38) |
| ClinVar | [VCV6759](https://www.ncbi.nlm.nih.gov/clinvar/variation/6759/) |

**All HGVS expressions:** `NC_000002.11:g.111395730del`, `NC_000002.12:g.110638153del`, `NG_012048.1:g.44954del`, `NM_001278616.2:c.3009del`, `NM_001278617.2:c.2898del`, `NM_004336.5:c.3069del`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 8.242, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.727, pLI 7.3293e-13. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in the last exon (25 of 25)** — predicted to **escape NMD**, so the truncated protein is likely expressed. An input to PVS1, not an applied code.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**BUB1** population constraint: LOEUF 0.727, pLI 7.3293e-13, missense-Z 1.4894. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **colorectal cancer** — Limited (AD)

## Protein context {#protein}

Residue **1024** lies in the protein kinase domain.

AlphaFold model confidence (whole protein): pLDDT 63.91, 31% of residues very-high.

**11 experimental structure(s)** (PDB): [2LAH](https://www.rcsb.org/structure/2LAH), [4A1G](https://www.rcsb.org/structure/4A1G), [4QPM](https://www.rcsb.org/structure/4QPM), [4R8Q](https://www.rcsb.org/structure/4R8Q), [5DMZ](https://www.rcsb.org/structure/5DMZ), [6F7B](https://www.rcsb.org/structure/6F7B).

## What this gene does {#gene-function}

*Describes the biological roles of BUB1 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** BUB1's established molecular role includes protein kinase activity. p.His1024fs falls in the protein kinase domain.


### Pathways affected {#pathways}

BUB1 participates in **6 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Amplification  of signal from unattached  kinetochores via a MAD2  inhibitory signal](https://reactome.org/content/detail/R-HSA-141444) | curated |
| [EML4 and NUDC in mitotic spindle formation](https://reactome.org/content/detail/R-HSA-9648025) | curated |
| [Mitotic Prometaphase](https://reactome.org/content/detail/R-HSA-68877) | curated |
| [RHO GTPases Activate Formins](https://reactome.org/content/detail/R-HSA-5663220) | curated |
| [Resolution of Sister Chromatid Cohesion](https://reactome.org/content/detail/R-HSA-2500257) | curated |
| [Separation of Sister Chromatids](https://reactome.org/content/detail/R-HSA-2467813) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** protein kinase activity, protein serine/threonine kinase activity, histone H2A kinase activity.

**Biological process:** regulation of sister chromatid cohesion, mitotic spindle assembly checkpoint signaling, regulation of chromosome segregation, positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric.

## Clinical significance {#significance}

**Pathogenic** — review status No assertion criteria *(no assertion criteria provided)*, last evaluated 1998-03-19.

**Submitter consensus:** unanimous (1/1 Pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| OMIM | Pathogenic | no assertion criteria provided | literature only | 1998-03-19 |

## Associated conditions {#conditions}

[colon carcinoma](https://sugi.bio/atlas/disease/colon-carcinoma/).

**Reported phenotype names (ClinVar):** Carcinoma of colon, Colonic carcinoma, Colon carcinoma.

## Similar variants {#similar}

Related BUB1 variant pages (same residue, condition, or type): [BUB1 p.His1024Arg](/variant/bub1-p-his1024arg), [BUB1 p.His1024Leu](/variant/bub1-p-his1024leu), [BUB1 p.Gln170fs](/variant/bub1-p-gln170fs), [BUB1 p.Gln503fs](/variant/bub1-p-gln503fs), [BUB1 p.Lys1053fs](/variant/bub1-p-lys1053fs), [BUB1 c.1699-20del](/variant/bub1-c-1699-minus-20del), [BUB1 c.567+7del](/variant/bub1-c-567-plus-7del), [BUB1 c.958-15del](/variant/bub1-c-958-minus-15del).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 6759). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*