CSDE1

Chr 1

cold shock domain containing E1

Also known as: D1S155E, UNR

NCBI Gene: 7812 ENSG00000009307 UniProt: O75534 OMIM: 191510

The CSDE1 protein is an RNA-binding protein that regulates mRNA stability and translation, and is required for stress granule formation during cellular stress. Mutations cause autosomal dominant neurodevelopmental disorders with intellectual disability, developmental delay, and variable features including seizures and behavioral abnormalities. This gene is highly constrained against loss-of-function variants in the population, indicating that such mutations are likely to be pathogenic.

OMIM ResearchSummary from RefSeq, UniProt

Enables RISC complex binding activity; RNA stem-loop binding activity; and lncRNA binding activity. Involved in IRES-dependent viral translational initiation; regulation of gene expression; and stress granule assembly. Located in cytosol. Part of CRD-mediated mRNA stability complex. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Clinical highlights

Gene–disease validity (ClinGen)

Definitive · complex neurodevelopmental disorder · AD · ClinGen 2023

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.14

LOEUF· LoF intol.

LOF

Mechanism· G2P

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.14LOEUF

pLI 1.000

Z-score 5.85

OE 0.05 (0.02–0.14)

Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?

3.45Z-score

OE missense 0.55 (0.50–0.61)

259 obs / 469.5 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.05 (0.02–0.14)

0≤0.351.4

Missense OE?0.55 (0.50–0.61)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 2 / 43.8Missense obs/exp: 259 / 469.5Syn Z: 0.40

Background carrier burden — how many people carry a rare variant somewhere in CSDE1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 140

758 rare PASS variants

Rare truncating (LoF)

1 in 2,800

59 rare PASS variants

Rare synonymous (reference)

1 in 100

354 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CSDE1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

Exome coverage (gnomAD): All 18 coding exons well covered in gnomAD exomes and genomes.? see exons ↓