GEO series

Molecular consequences of a PHF21A variant, c.1285G>A, associated with autism spectrum disorder

GSE290591 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/04/10 Platform GPL15520

At a glance

RNA-seq (gene expression) · human · 10 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: 10 samples: 2 × 293T,wt, vs 2 × 293T,mut, vs 2 × neurons,wt, vs 2 × neurons,mut,Groups 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: Molecular Consequences of a Missense PHF21A Variant, c.1285G > A, Associated With Syndromic Neurodevelopmental DisorderCellular and molecular neurobiology · 2025

Summary (written by the submitters)

PHF21A is a histone reader protein that recognizes unmethylated H3 lysine 4 and binds to DNA through its AT-hook motif. PHF21A heterozygosity is associated with intellectual disability, behavioral issues, and craniofacial dysmorphism, with or without seizures (IDDBCS), also known as PHF21A-related neurodevelopmental disorders. To date, the only missense variant associated with PHF21A-related disorders is c.1285G>A, which substitutes one of the core amino acids consisting of the AT-hook motif.

Read the full summary ↓

This variant, located at the last nucleotide of exon 13, potentially disrupt both alternative splicing and the DNA binding function, providing a unique opportunity to investigate the molecular mechanisms underlying PHF21A-related disorders. Here, we systematically investigated the consequences of this variant on mRNA splicing and DNA binding. Our results indicate that the variant significantly reduced the splicing efficiency of PHF21A isoforms while maintaining DNA binding capability. Thus, reduced dosage rather than impaired DNA binding likely contributes to the cognitive impairments seen in the individual with this variant.

Published in

Molecular Consequences of a Missense PHF21A Variant, c.1285G > A, Associated With Syndromic Neurodevelopmental Disorder

Gavilan CM, Murata-Nakamura Y, Porter R et al. · Cellular and molecular neurobiology 2025 · PMID 40622422 · doi:10.1007/s10571-025-01584-8

This dataset

Open GSE290591 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 GSE290591_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 PRJNA1228686 and SRA study SRP566544. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40622422) ↗

Study design

2 × 293T,wt, vs 2 × 293T,mut, vs 2 × neurons,wt, vs 2 × neurons,mut,

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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

GSM8817795 293T,wt,rep1 293T,wt,
GSM8817796 293T,mut,rep1 293T,mut,
GSM8817797 293T,wt,rep2 293T,wt,
GSM8817798 293T,mut,rep2 293T,mut,
GSM8817799 neurons,wt,rep1 neurons,wt,
GSM8817800 neurons,mut,rep1 neurons,mut,
GSM8817801 neurons,wt,rep2 neurons,wt,
GSM8817802 neurons,mut,rep2 neurons,mut,
GSM8890760 Ex12-15, wt
GSM8890761 Ex12-15, variant

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