GeneBe

CELF1

protein-coding

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

Gene summary

Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. This gene may play a role in myotonic dystrophy type 1 (DM1) via interactions with the dystrophia myotonica-protein kinase (DMPK) gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

Previous symbols:
  • CUGBP1

MANE transcript

NM_001376376.1

Inheritance

—

ClinVar variants

U:45B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr11:47,465,933-47,565,569

External References & Databases

Ensembl (ENSG00000149187)NCBI Gene (10658)OMIM (601074)HGNC:2549GenCCUniProt (Q92879)AlphaFoldClinVar (CELF1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~99.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CELF1 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 34
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001376376.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
 2
missense
36
clinvar
 36
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
7
clinvar
 7
Total00450146
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 178 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001376376.1RefSeqNP_001363305.113MANE Select
ENST00000687097.1EnsemblENSP00000508525.113MANE Select
NM_001025596.3RefSeqNP_001020767.112Standard
NM_001172639.2RefSeqNP_001166110.113Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
celf1Danio rerio

Structure: endodermal cell

Quality: process quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Adipogenesis
  • mRNA Processing

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

Molecular Function

  • translation repressor activity, mRNA regulatory element binding
  • RNA binding
  • mRNA binding
  • protein binding
  • pre-mRNA binding

Cellular Component

  • nucleus
  • nucleoplasm
  • cytoplasm
  • membrane
  • ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000532048
Coding exons
13
Length
99626
Individuals with no LoFs
125720
Homozygous LoFs
0
Heterozygous LoFs
3
Defined
125723
p
0.0000119
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.341282880.4450.00001493387
Missense (PolyPhen)2661.110.42546675
Synonymous1.14911060.8590.00000602957
Loss of Function4.71127.80.03600.00000135307

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000260.000026rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.156

Intolerance Scores

LoFtool
0.419
RVIS EVS
-0.49
RVIS percentile EVS
22.09

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
H
Indispensability pred.
E
Indispensability score
0.781

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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