GEO series

Novel variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders

GSE287369 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2026/01/31 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 15 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 15 samples: 5 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: De novo variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disordersNature communications · 2026

Summary (written by the submitters)

SF3B1 is an essential and ubiquitous splicing factor that plays a pivotal role in the early steps of pre-mRNA splicing. Recurrent somatic missense mutations in SF3B1 are frequent in cancers, but no constitutional variant has been reported so far. We describe here a cohort of 26 individuals with neurodevelopmental disorders, harbouring SF3B1 constitutional heterozygous variants that appeared mostly de novo.

Read the full summary ↓

Patients present with a global developmental delay, associated with variable neurological and facial dysmorphic traits. A dichotomy may emerge between patients harbouring predicted loss of function (n=9) and missense variants (n=17), the latter being associated with a more severe and syndromic phenotype, including heart and gastrointestinal anomalies. We focused on de novo SF3B1 missense variants, which were largely distinct from those reported in cancer. Functional complementation assays show that de novo SF3B1 missense variants did not cause a loss of function of the protein. Targeted and genome-wide analysis of RNA splicing reveal that they affect canonical and alternative splicing more moderately than somatic variants, and subtly modify the splicing of many transcripts, some of which are involved in neurodevelopmental disorders. SF3B1 joins the short list of U2 snRNP components involved in both cancer and neurodevelopmental disorders.

Published in

De novo variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders

Uguen K, Bergot T, Scott-Boyer MP et al. · Nature communications 2026 · PMID 41577671 · doi:10.1038/s41467-026-68284-9

This dataset

Open GSE287369 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE287369_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1212504 and SRA study SRP558234. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41577671) ↗

Study design

5 conditions, mostly in triplicate

WT ×3 K700E ×3 E722K ×3 N829S ×3 P780L ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8744960 WT_1 WT
GSM8744961 WT_2 WT
GSM8744962 WT_3 WT
GSM8744963 K700E_1 K700E
GSM8744964 K700E_2 K700E
GSM8744965 K700E_3 K700E
GSM8744966 E722K_1 E722K
GSM8744967 E722K_2 E722K
GSM8744968 E722K_3 E722K
GSM8744969 N829S_1 N829S
GSM8744970 N829S_2 N829S
GSM8744971 N829S_3 N829S
GSM8744972 P780L_1 P780L
GSM8744973 P780L_2 P780L
GSM8744974 P780L_3 P780L

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