CELF3

CUGBP Elav-like family member 3, the group of RNA binding motif containing

Basic information

Region (hg38): 1:151700058-151716803

Previous symbols: [ "TNRC4" ]

Links

ENSG00000159409 ∙ NCBI:11189 ∙ OMIM:612678 ∙ HGNC:11967 ∙ Uniprot:Q5SZQ8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CELF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELF3 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				1		1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in CELF3

This is a list of pathogenic ClinVar variants found in the CELF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151705100-C-T		not specified	Uncertain significance (Jun 12, 2023)
1-151705848-C-A		not specified	Uncertain significance (Feb 28, 2024)
1-151705909-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-151706324-C-T			Likely benign (Sep 01, 2022)
1-151706347-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-151706690-C-T		not specified	Uncertain significance (Oct 05, 2021)
1-151706722-G-A		not specified	Uncertain significance (Jun 21, 2022)
1-151707241-C-T		not specified	Uncertain significance (May 16, 2024)
1-151707576-C-T		not specified	Uncertain significance (May 24, 2023)
1-151707796-T-A			Uncertain significance (Oct 22, 2020)
1-151709048-C-T		not specified	Uncertain significance (Apr 09, 2022)
1-151709291-C-T		not specified	Uncertain significance (Jun 09, 2022)
1-151714604-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-151715887-C-A		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELF3	protein_coding	protein_coding	ENST00000290583	12	14411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.768	0.232	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.30	121	275	0.440	0.0000163	2997
Missense in Polyphen		44	110.3	0.39892		1207
Synonymous	1.20	102	119	0.860	0.00000810	896
Loss of Function	3.90	5	26.8	0.187	0.00000150	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein involved in the regulation of pre- mRNA alternative splicing. 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 cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA. {ECO:0000269|PubMed:11158314, ECO:0000269|PubMed:15009664}.
• Pathway: Preimplantation Embryo (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.296
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.710
• hipred: Y
• hipred_score: 0.711
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Celf3
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA splice site selection;spermatogenesis;RNA splicing;flagellated sperm motility;nuclear body organization;positive regulation of mRNA splicing, via spliceosome;ncRNA transcription
• Cellular component: nucleus;cytoplasm;nuclear body;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;pre-mRNA binding;7SK snRNA binding