CELF2

CUGBP Elav-like family member 2, the group of RNA binding motif containing

Basic information

Region (hg38): 10:10798397-11336675

Previous symbols: [ "CUGBP2" ]

Links

ENSG00000048740 ∙ NCBI:10659 ∙ OMIM:602538 ∙ HGNC:2550 ∙ Uniprot:O95319 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
• complex neurodevelopmental disorder (Limited), mode of inheritance: AD
• developmental and epileptic encephalopathy 97 (Strong), mode of inheritance: AD
• neurodevelopmental disorder (Strong), mode of inheritance: AD
• developmental and epileptic encephalopathy 97 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 97	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	33131106

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CELF2 gene.

• Developmental and epileptic encephalopathy 97 (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELF2 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						0
missense	2	1	33	1		37
nonsense	2					2
start loss			1			1
frameshift	1	2	3			6
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	5	3	39	1	0

Variants in CELF2

This is a list of pathogenic ClinVar variants found in the CELF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-10798774-T-G		CELF2-related disorder	Likely benign (Mar 21, 2023)
10-10846131-G-A			Likely benign (Apr 01, 2023)
10-10919970-G-A			Likely benign (Feb 01, 2023)
10-10920008-G-A			Benign (Dec 31, 2019)
10-11005416-T-G			Uncertain significance (Jul 01, 2024)
10-11005419-G-T			Uncertain significance (Jul 10, 2024)
10-11005437-T-C		CELF2-related disorder	Likely benign (May 06, 2022)
10-11005441-G-A			Uncertain significance (May 13, 2022)
10-11018091-T-A		CELF2-related disorder	Uncertain significance (Jan 03, 2023)
10-11018150-G-A			Uncertain significance (Feb 02, 2024)
10-11165517-T-A			Uncertain significance (Jun 07, 2024)
10-11165538-G-A			Uncertain significance (Oct 14, 2022)
10-11165616-C-T		not specified	Uncertain significance (Sep 30, 2024)
10-11165632-A-G		Neurodevelopmental disorder	Uncertain significance (Jun 19, 2024)
10-11165651-G-GGACCGGAGTCAGAACCCTCCGC		Developmental and epileptic encephalopathy 97	Likely pathogenic (-)
10-11165656-G-A			Uncertain significance (Jan 12, 2022)
10-11165665-A-G			Uncertain significance (Jan 14, 2024)
10-11217436-G-T		not specified	Uncertain significance (Mar 29, 2024)
10-11217442-T-G		Developmental and epileptic encephalopathy 97	Uncertain significance (-)
10-11217470-CCCAGAATG-C			Uncertain significance (Jul 23, 2024)
10-11249201-G-A			Uncertain significance (Nov 22, 2023)
10-11257815-C-T		not specified	Uncertain significance (Oct 28, 2024)
10-11257836-T-A			Uncertain significance (Jun 01, 2022)
10-11257840-G-A			Uncertain significance (Feb 24, 2023)
10-11266630-A-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELF2	protein_coding	protein_coding	ENST00000450189	13	331416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000355	119615	0	5	119620	0.0000209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.34	88	299	0.294	0.0000159	3414
Missense in Polyphen		13	107.43	0.12101		1258
Synonymous	-0.448	123	117	1.05	0.00000696	1014
Loss of Function	4.66	1	27.2	0.0368	0.00000123	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000944	0.0000944
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000181	0.0000181
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of TNNT2 in embryonic, but not adult, skeletal muscle. Activates TNNT2 exon 5 inclusion by antagonizing the repressive effect of PTB. Acts as both an activator and repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Promotes inclusion of exonS 21 and exclusion of exon 5 of the NMDA receptor R1 pre- mRNA. Involved in the apoB RNA editing activity. Increases COX2 mRNA stability and inhibits COX2 mRNA translation in epithelial cells after radiation injury (By similarity). Modulates the cellular apoptosis program by regulating COX2-mediated prostaglandin E2 (PGE2) expression (By similarity). Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK. Binds to the muscle-specific splicing enhancer (MSE) intronic sites flanking the TNNT2 alternative exon 5. Binds preferentially to UG-rich sequences, in particular UG repeat and UGUU motifs. Binds to apoB mRNA, specifically to AU-rich sequences located immediatly upstream of the edited cytidine. Binds AU-rich sequences in the 3'-UTR of COX2 mRNA (By similarity). Binds to an intronic RNA element responsible for the silencing of exon 21 splicing (By similarity). Binds to (CUG)n repeats (By similarity). May be a specific regulator of miRNA biogenesis. Binds to primary microRNA pri-MIR140 and, with CELF1, negatively regulates the processing to mature miRNA (PubMed:28431233). {ECO:0000250|UniProtKB:Q9Z0H4, ECO:0000269|PubMed:11158314, ECO:0000269|PubMed:11577082, ECO:0000269|PubMed:11931771, ECO:0000269|PubMed:12649496, ECO:0000269|PubMed:14973222, ECO:0000269|PubMed:15657417, ECO:0000269|PubMed:15894795, ECO:0000269|PubMed:28431233}.
• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.213
• hipred: Y
• hipred_score: 0.728
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Celf2

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA splice site selection;RNA processing;regulation of heart contraction
• Cellular component: nucleus;cytoplasm;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;pre-mRNA binding