# NM_001211.6(BUB1B):c.1302del (p.Ser435fs)

https://sugi.bio/variant/bub1b-p-ser435fs

## Summary

**BUB1B p.Ser435fs (c.1302del)** is classified **Pathogenic** in BUB1B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-06). Very rare (popmax 8.48e-05%, nfe); Associated with mosaic variegated aneuploidy syndrome 1.

**At a glance:** Pathogenic · review: Single submitter · rsID rs2542554755 · 1 submitter · 1 linked condition · very rare (popmax 8.48e-05%, nfe)

## For patients & families {#patients}

This is a change in the BUB1B gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, and is linked to mosaic variegated aneuploidy syndrome 1.

*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.*

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0024694/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [BUB1B](https://sugi.bio/atlas/gene/BUB1B/) |
| Protein change (HGVS p.) | p.Ser435fs |
| Coding change (HGVS c.) | c.1302del |
| MANE Select transcript | [NM_001211](https://www.ncbi.nlm.nih.gov/nuccore/NM_001211) |
| dbSNP | [rs2542554755](https://www.ncbi.nlm.nih.gov/snp/rs2542554755/) |
| Variant type | Deletion |
| Location | chr15:40199627-40199627 (GRCh38) |
| ClinVar | [VCV3018326](https://www.ncbi.nlm.nih.gov/clinvar/variation/3018326/) |

**All HGVS expressions:** `LRG_489:g.43620del`, `LRG_489t1:c.1302del`, `NC_000015.10:g.40199628del`, `NC_000015.9:g.40491829del`, `NG_016338.1:g.43620del`, `NM_001211.6:c.1302del`

## 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 5.442, GERP 1.92, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.707, pLI 2.5766e-14. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 10 of 23**, so the transcript is predicted to undergo NMD.
- 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 (gnomAD v4.1): grpmax **8.48e-05%** (nfe) · 1/1,179,840 in the highest group · 1/1,461,588 alleles overall — very rare (popmax 8.48e-05%, nfe).

*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}

**BUB1B** population constraint: LOEUF 0.707, pLI 2.5766e-14, missense-Z 1.7805; ClinGen dosage — haploinsufficiency 30, triplosensitivity 0 (0–3 scale). *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):

- **mosaic variegated aneuploidy syndrome 1** — Definitive (AR)

## Protein context {#protein}

Residue **435** lies in a modified residue (phosphoserine).

AlphaFold model confidence (whole protein): pLDDT 64.62, 15% of residues very-high.

**9 experimental structure(s)** (PDB): [2WVI](https://www.rcsb.org/structure/2WVI), [3SI5](https://www.rcsb.org/structure/3SI5), [4GGD](https://www.rcsb.org/structure/4GGD), [5JJA](https://www.rcsb.org/structure/5JJA), [5K6S](https://www.rcsb.org/structure/5K6S), [5KHU](https://www.rcsb.org/structure/5KHU) — incl. mutant structure 5KHU.

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

*Describes the biological roles of BUB1B (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.*


### Pathways affected {#pathways}

BUB1B participates in **10 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [APC-Cdc20 mediated degradation of Nek2A](https://reactome.org/content/detail/R-HSA-179409) | curated |
| [APC/C:Cdc20 mediated degradation of mitotic proteins](https://reactome.org/content/detail/R-HSA-176409) | curated |
| [Amplification  of signal from unattached  kinetochores via a MAD2  inhibitory signal](https://reactome.org/content/detail/R-HSA-141444) | curated |
| [Cdc20:Phospho-APC/C mediated degradation of Cyclin A](https://reactome.org/content/detail/R-HSA-174184) | curated |
| [EML4 and NUDC in mitotic spindle formation](https://reactome.org/content/detail/R-HSA-9648025) | curated |
| [Inactivation of APC/C via direct inhibition of the APC/C complex](https://reactome.org/content/detail/R-HSA-141430) | 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}

**Biological process:** mitotic spindle assembly checkpoint signaling.

## Clinical significance {#significance}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-03-06.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2024-03-06 |

## Associated conditions {#conditions}

[mosaic variegated aneuploidy syndrome 1](https://sugi.bio/atlas/disease/mosaic-variegated-aneuploidy-syndrome-1/).

**Reported phenotype names (ClinVar):** Mosaic variegated aneuploidy syndrome 1, Warburton-Anyane-Yeboa syndrome.

## Similar variants {#similar}

Related BUB1B variant pages (same residue, condition, or type): [BUB1B p.Ala957fs](/variant/bub1b-p-ala957fs), [BUB1B p.Arg80_Tyr81insTer](/variant/bub1b-p-arg80-tyr81inster), [BUB1B p.His856fs](/variant/bub1b-p-his856fs), [BUB1B c.1628+24_1628+32del](/variant/bub1b-c-1628-plus-24-1628-plus-32del), [BUB1B p.Ala332fs](/variant/bub1b-p-ala332fs), [BUB1B p.Arg104fs](/variant/bub1b-p-arg104fs), [BUB1B p.Arg349fs](/variant/bub1b-p-arg349fs), [BUB1B p.Arg381fs](/variant/bub1b-p-arg381fs).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-06); 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 2026-07-14); 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 3018326). 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.*