CELF6

CUGBP Elav-like family member 6, the group of RNA binding motif containing

Basic information

Region (hg38): 15:72284727-72320157

Previous symbols: [ "BRUNOL6" ]

Links

ENSG00000140488 ∙ NCBI:60677 ∙ OMIM:612681 ∙ HGNC:14059 ∙ Uniprot:Q96J87 ∙ 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 CELF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELF6 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			16	1	2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	16	2	3

Variants in CELF6

This is a list of pathogenic ClinVar variants found in the CELF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-72287285-C-A		not specified	Uncertain significance (Jul 30, 2023)
15-72287320-A-G		not specified	Uncertain significance (Oct 18, 2021)
15-72288338-C-T		not specified	Uncertain significance (May 16, 2024)
15-72288458-G-A			Benign (Jun 08, 2018)
15-72288551-C-G		not specified	Uncertain significance (May 09, 2023)
15-72288877-G-A		not specified	Uncertain significance (Oct 29, 2021)
15-72288925-T-G		not specified	Uncertain significance (Sep 22, 2022)
15-72288930-G-T		not specified	Uncertain significance (Jul 26, 2022)
15-72289162-T-G		CELF6-related disorder	Likely benign (Jun 23, 2018)
15-72289243-G-T		not specified	Uncertain significance (Jan 10, 2022)
15-72289429-T-A		not specified	Uncertain significance (Jul 09, 2021)
15-72289646-C-A		not specified	Uncertain significance (Feb 28, 2023)
15-72289659-G-T		not specified	Uncertain significance (Jun 16, 2024)
15-72289685-A-C		not specified	Uncertain significance (Dec 21, 2023)
15-72289733-G-C		not specified	Uncertain significance (Dec 09, 2023)
15-72289946-G-A		not specified	Uncertain significance (Sep 27, 2021)
15-72290008-A-C		not specified	Uncertain significance (Aug 02, 2022)
15-72304751-C-T		not specified	Uncertain significance (Oct 05, 2023)
15-72304807-G-A		not specified	Likely benign (Apr 28, 2017)
15-72315900-C-T		not specified	Uncertain significance (Jun 24, 2022)
15-72319756-A-G			Benign (Jul 10, 2018)
15-72319775-G-A		not specified	Uncertain significance (Aug 08, 2023)
15-72319783-C-A			Benign (Jul 06, 2018)
15-72319854-C-T		CELF6-related disorder	Benign (May 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELF6	protein_coding	protein_coding	ENST00000287202	12	35403

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00445	0.994	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	163	284	0.573	0.0000177	3044
Missense in Polyphen		34	62.807	0.54134		640
Synonymous	2.32	94	127	0.738	0.00000915	996
Loss of Function	2.81	8	22.4	0.358	0.00000119	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000934	0.0000924
European (Non-Finnish)	0.0000269	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 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 TNNT2 in a muscle-specific splicing enhancer (MSE)-dependent manner. Promotes also exon exclusion of INSR pre-mRNA. {ECO:0000269|PubMed:14761971}.

Intolerance Scores

• loftool: 0.547
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.278
• hipred: N
• hipred_score: 0.455
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Celf6
• Phenotype: normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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; homeostasis/metabolism phenotype

Gene ontology

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