CSDE1

protein-coding

cold shock domain containing E1

Gene summary

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]

MANE transcript

NM_001007553.3

Inheritance

ClinVar variants

P:17U:153B:25

Top phenotype

complex neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr1:114,716,913-114,758,676

External References & Databases

Ensembl (ENSG00000009307)

Transcript & Mutation Effects

hg38 • Region Span ~41.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: ClinGen

*CSDE1* was first reported in relation to autosomal dominant complex neurodevelopmental disorder in 2019 (Guo et al., PMID: 31579823). *CSDE1*-related complex neurodevelopmental disorder is characterized by autism, intellectual disability, delayed speech and delayed motor development. Less frequently reported phenotypes include sleep disturbances, obsessive behavior, hypotonia and short stature. Fifteen variants (nonsense, frameshift, splicing) that have been reported in 18 probands in 3 publications (PMIDs: 31579823, 33867523, 34519148) are included in this curation. One recurrent variant (c.367C>T, p.R123*) is found in four unrelated families. Three of the variants are inherited. Each of the carrier parents and siblings either exhibited mild neurodevelopmental phenotypes or presented with substantial family history of autism or developmental disability. More evidence is available in the literature, but the maximum score for genetic evidence (12 points) has been reached. The mechanism of pathogenicity appears to be loss-of-function. This gene-disease relationship is also supported by animal models and *in vitro* functional assays (PMID: 31579823). *Csde1* knockdown in primary mouse cortical neurons leads to neurite overgrowth, abnormal dendritic spine morphology/synapse formation, and impaired synaptic transmission. Additionally, disruption of the *Csde1* homolog gene *dUnr* in Drosophila interferes with synapse development and transmission (PMID: 31579823). The results in Drosophila models are consistent with the effect of *CSDE1* deficiency on synapse development and function in humans. In summary, there is definitive evidence supporting the relationship between *CSDE1* and autosomal dominant complex neurodevelopmental disorder. This classification was approved by the ClinGen Intellectual Disability and Autism Gene Curation Expert Panel on November 21, 2023 (SOP Version 10).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CSDE1 variants in ClinVar

12 Conditions Cataloged

not providedTotal: 91

Inborn genetic diseasesTotal: 74

CSDE1-related disorderTotal: 28

not specifiedTotal: 13

CSDE1-associated disorderTotal: 2

Complex neurodevelopmental disorderTotal: 2

AutismTotal: 1

CSDE1-related neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001007553.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	14 clinvar	3 clinvar	22
missense		3 clinvar	122 clinvar	8 clinvar		133
nonsense	3 clinvar	4 clinvar	3 clinvar			10
start loss			1 clinvar			1
frameshift	4 clinvar	2 clinvar	5 clinvar			11
splice donor/acceptor (+/-2bp)	1 clinvar		17 clinvar			18
Total	8	9	153	22	3	195

Highest pathogenic variant AF is 0.0000032247538

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 345 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001007553.3	RefSeq	NP_001007554.1	18	MANE Select
ENST00000358528.9	Ensembl	ENSP00000351329.4	18	MANE Select
NM_001130523.3	RefSeq	NP_001123995.1	18	Standard
NM_001242891.2	RefSeq	NP_001229820.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
miR-targeted genes in squamous cell - TarBase
Validated targets of C-MYC transcriptional repression

Biological Process

regulation of transcription, DNA-templated
male gonad development
nuclear-transcribed mRNA catabolic process, no-go decay

Molecular Function

DNA binding
RNA binding
protein binding

Cellular Component

Golgi apparatus
cytosol
plasma membrane
CRD-mediated mRNA stability complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000438362
Coding exons: 19
Length: 41764
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125747
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.45	259	469	0.552	0.0000252	5578
Missense (PolyPhen)		53	155.68	0.34043		1836
Synonymous	0.403	155	162	0.960	0.00000829	1619
Loss of Function	5.85	2	43.8	0.0456	0.00000253	510

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA-binding protein. Required for internal initiation of translation of human rhinovirus RNA. May be involved in translationally coupled mRNA turnover. Implicated with other RNA- binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding- region determinant of instability (mCRD) domain. {ECO:0000269|PubMed:11051545, ECO:0000269|PubMed:15314026}.;

Recessive Scores

pRec: 0.178

Intolerance Scores

LoFtool: 0.0149
RVIS EVS: -1
RVIS percentile EVS: 8.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.998

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium