CELF4

CUGBP Elav-like family member 4, the group of RNA binding motif containing

Basic information

Region (hg38): 18:37243039-37565827

Previous symbols: [ "BRUNOL4" ]

Links

ENSG00000101489 ∙ NCBI:56853 ∙ OMIM:612679 ∙ HGNC:14015 ∙ Uniprot:Q9BZC1 ∙ 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 CELF4 gene.

• Inborn genetic diseases (16 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELF4 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	3	4
missense			11	5		16
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	13	6	3

Variants in CELF4

This is a list of pathogenic ClinVar variants found in the CELF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-37259255-C-A		not specified	Uncertain significance (Feb 16, 2023)
18-37264681-C-G		CELF4-related disorder	Uncertain significance (Nov 06, 2023)
18-37264705-C-T		CELF4-related disorder	Benign/Likely benign (Dec 31, 2019)
18-37264706-G-A		not specified	Uncertain significance (May 17, 2023)
18-37266555-G-A			Benign (Aug 03, 2018)
18-37266557-C-T		not specified	Uncertain significance (Mar 24, 2023)
18-37266576-G-T		not specified	Uncertain significance (Apr 13, 2021)
18-37266581-C-T		not specified	Likely benign (Sep 07, 2022)
18-37270793-G-A		CELF4-related disorder	Likely benign (Aug 15, 2019)
18-37270806-G-A		not specified	Uncertain significance (Jul 12, 2022)
18-37270831-G-A		not specified	Uncertain significance (Sep 17, 2021)
18-37270840-C-T		not specified	Likely benign (Apr 11, 2023)
18-37270855-C-T		CELF4-related disorder	Likely benign (Feb 03, 2021)
18-37270882-C-T		not specified	Uncertain significance (Dec 16, 2023)
18-37270883-G-A		CELF4-related disorder	Benign (Oct 18, 2019)
18-37273013-C-T		not specified	Likely benign (Jul 08, 2022)
18-37273035-T-C		CELF4-related disorder	Likely benign (May 01, 2019)
18-37273065-C-T			Likely benign (Apr 01, 2023)
18-37273085-C-T		not specified	Likely benign (Feb 15, 2023)
18-37273127-C-T		not specified	Likely benign (Feb 16, 2023)
18-37273128-G-A		CELF4-related disorder	Likely benign (Jul 19, 2019)
18-37273157-G-A			Uncertain significance (Jan 23, 2023)
18-37274304-C-T		CELF4-related disorder	Benign (Mar 01, 2019)
18-37274316-G-A			Uncertain significance (Jun 06, 2023)
18-37274320-G-T		Developmental disorder	Likely pathogenic (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELF4	protein_coding	protein_coding	ENST00000420428	12	322991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00183	125593	0	5	125598	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.16	157	315	0.499	0.0000179	3208
Missense in Polyphen		59	152.94	0.38578		1558
Synonymous	1.05	116	131	0.884	0.00000891	903
Loss of Function	4.48	2	27.2	0.0735	0.00000154	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.000125	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000208	0.0000176
Middle Eastern	0.000125	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein implicated 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. Promotes exclusion of both the smooth muscle (SM) and non-muscle (NM) exons in actinin pre-mRNAs. 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:12649496, ECO:0000269|PubMed:14973222, ECO:0000269|PubMed:15009664, ECO:0000269|PubMed:15894795}.
• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.344
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.516
• hipred: Y
• hipred_score: 0.743
• ghis: 0.688

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Celf4
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary 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); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;regulation of alternative mRNA splicing, via spliceosome;mRNA splice site selection;germ cell development;embryo development ending in birth or egg hatching;negative regulation of translation;negative regulation of mRNA splicing, via spliceosome;positive regulation of mRNA splicing, via spliceosome;negative regulation of excitatory postsynaptic potential;regulation of retina development in camera-type eye
• Cellular component: nucleus;cytoplasm;ribonucleoprotein complex
• Molecular function: translation repressor activity, mRNA regulatory element binding;RNA binding;mRNA binding;pre-mRNA binding;BRE binding