CSDE1

cold shock domain containing E1

Basic information

Region (hg38): 1:114716913-114758676

Links

ENSG00000009307 ∙ NCBI:7812 ∙ OMIM:191510 ∙ HGNC:29905 ∙ Uniprot:O75534 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Definitive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSDE1 gene.

• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSDE1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					4	4
missense		1	76	5		82
nonsense	1	2	1			4
start loss			1			1
frameshift	2	1	4			7
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region			2		2	4
non coding			3	1	1	5
Total	4	4	86	6	5

Highest pathogenic variant AF is 0.0000131

Variants in CSDE1

This is a list of pathogenic ClinVar variants found in the CSDE1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-114716959-T-C			Likely benign (Jun 23, 2018)
1-114716978-G-T			Benign (Jun 13, 2019)
1-114718159-G-C		CSDE1-related disorder	Likely benign (Jul 24, 2019)
1-114718188-T-G		Inborn genetic diseases	Uncertain significance (May 17, 2024)
1-114718191-CG-C			Uncertain significance (Aug 30, 2022)
1-114718204-C-G			Uncertain significance (Apr 21, 2021)
1-114718221-G-A		CSDE1-related disorder	Likely benign (Mar 16, 2022)
1-114718221-G-T		Inborn genetic diseases • CSDE1-related disorder	Benign (Dec 09, 2021)
1-114718222-G-T		Inborn genetic diseases	Uncertain significance (Sep 19, 2022)
1-114718626-G-C		CSDE1-associated neurodevelopmental disorder	Uncertain significance (Jun 11, 2021)
1-114718641-C-T		CSDE1-related disorder	Uncertain significance (Aug 02, 2023)
1-114718642-G-A			Uncertain significance (May 25, 2022)
1-114718744-C-G		Inborn genetic diseases	Uncertain significance (Jun 17, 2024)
1-114719589-A-G		Inborn genetic diseases	Uncertain significance (Jan 07, 2025)
1-114719648-T-C			Uncertain significance (Mar 03, 2023)
1-114719654-C-G		Inborn genetic diseases	Uncertain significance (Nov 08, 2024)
1-114719661-G-A		CSDE1-associated disorder	Likely pathogenic (Jul 21, 2020)
1-114719693-T-C			Uncertain significance (Jun 05, 2024)
1-114719698-A-G		CSDE1-related disorder	Benign (Dec 01, 2022)
1-114719725-ATAGT-A			Pathogenic (Mar 14, 2025)
1-114719746-A-G			Benign (May 18, 2018)
1-114720531-G-A		CSDE1-related disorder	Likely benign (Aug 08, 2019)
1-114720570-C-T			Uncertain significance (Sep 19, 2024)
1-114720582-A-T			Uncertain significance (Aug 23, 2024)
1-114720589-A-G			Uncertain significance (Aug 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSDE1	protein_coding	protein_coding	ENST00000438362	19	41764

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000368	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.45	259	469	0.552	0.0000252	5578
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.0149
• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.712
• hipred: Y
• hipred_score: 0.673
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csde1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;male gonad development;nuclear-transcribed mRNA catabolic process, no-go decay
• Cellular component: Golgi apparatus;cytosol;plasma membrane;CRD-mediated mRNA stability complex
• Molecular function: DNA binding;RNA binding;protein binding