CELF1

CUGBP Elav-like family member 1, the group of RNA binding motif containing

Basic information

Region (hg38): 11:47465932-47565569

Previous symbols: [ "CUGBP1" ]

Links

ENSG00000149187 ∙ NCBI:10658 ∙ OMIM:601074 ∙ HGNC:2549 ∙ Uniprot:Q92879 ∙ 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 CELF1 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELF1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in CELF1

This is a list of pathogenic ClinVar variants found in the CELF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47472254-C-T			Benign (Apr 06, 2018)
11-47472307-T-C		not specified	Uncertain significance (Jan 22, 2024)
11-47475437-T-C		not specified	Uncertain significance (Jun 13, 2023)
11-47475443-T-C		not specified	Uncertain significance (Jul 13, 2022)
11-47475503-C-T		not specified	Uncertain significance (Aug 12, 2022)
11-47476863-T-C		not specified	Uncertain significance (Jul 14, 2021)
11-47483512-T-C		not specified	Uncertain significance (Mar 03, 2022)
11-47484404-C-T		not specified	Uncertain significance (Apr 13, 2023)
11-47484460-C-T		not specified	Uncertain significance (Jan 23, 2023)
11-47486784-T-C		not specified	Uncertain significance (Feb 27, 2023)
11-47486786-T-C		not specified	Uncertain significance (Nov 08, 2022)
11-47487214-C-A		not specified	Uncertain significance (Feb 14, 2023)
11-47487214-C-T		not specified	Uncertain significance (Mar 24, 2023)
11-47488906-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-47488995-T-G		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELF1	protein_coding	protein_coding	ENST00000532048	13	99626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000286	125720	0	3	125723	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.34	128	288	0.445	0.0000149	3387
Missense in Polyphen		26	61.11	0.42546		675
Synonymous	1.14	91	106	0.859	0.00000602	957
Loss of Function	4.71	1	27.8	0.0360	0.00000135	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
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 cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. 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. Activates SM exon 5 inclusion by antagonizing the repressive effect of PTB. Promotes exclusion of exon 11 of the INSR pre-mRNA. Inhibits, together with HNRNPH1, insulin receptor (IR) pre-mRNA exon 11 inclusion in myoblast. Increases translation and controls the choice of translation initiation codon of CEBPB mRNA. Increases mRNA translation of CEBPB in aging liver (By similarity). Increases translation of CDKN1A mRNA by antagonizing the repressive effect of CALR3. Mediates rapid cytoplasmic mRNA deadenylation. Recruits the deadenylase PARN to the poly(A) tail of EDEN-containing mRNAs to promote their deadenylation. Required for completion of spermatogenesis (By similarity). Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK and to Bruno response elements (BREs). Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA. Binds to AU-rich sequences (AREs or EDEN-like) localized in the 3'-UTR of JUN and FOS mRNAs. Binds to the IR RNA. Binds to the 5'-region of CDKN1A and CEBPB mRNAs. Binds with the 5'-region of CEBPB mRNA in aging liver. May be a specific regulator of miRNA biogenesis. Binds to primary microRNA pri- MIR140 and, with CELF2, negatively regulates the processing to mature miRNA (PubMed:28431233). {ECO:0000250, ECO:0000269|PubMed:10536163, ECO:0000269|PubMed:11124939, ECO:0000269|PubMed:11158314, ECO:0000269|PubMed:12649496, ECO:0000269|PubMed:12799066, ECO:0000269|PubMed:14726956, ECO:0000269|PubMed:16601207, ECO:0000269|PubMed:16946708, ECO:0000269|PubMed:28431233}.
• Pathway: Adipogenesis;mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.419
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.913
• hipred: Y
• hipred_score: 0.696
• ghis: 0.689

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• 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: Celf1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: celf1
• Affected structure: endodermal cell
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA splice site selection;mRNA processing;germ cell development;embryo development ending in birth or egg hatching;RNA interference;negative regulation of translation;regulation of RNA splicing
• Cellular component: nucleus;nucleoplasm;cytoplasm;membrane;ribonucleoprotein complex
• Molecular function: translation repressor activity, mRNA regulatory element binding;RNA binding;mRNA binding;protein binding;pre-mRNA binding;BRE binding