ELAVL1
ELAV like RNA binding protein 1, the group of RNA binding motif containing
Basic information
Region (hg38): 19:7958573-8005659
Previous symbols: [ "HUR" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELAVL1 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 | 0 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 6 | 0 | 1 |
Variants in ELAVL1
This is a list of pathogenic ClinVar variants found in the ELAVL1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-7963566-T-A | not specified | Uncertain significance (May 09, 2022) | ||
| 19-7963637-A-C | not specified | Uncertain significance (Dec 20, 2023) | ||
| 19-7963692-C-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 19-7967548-G-A | Benign (Sep 26, 2019) | |||
| 19-7967683-T-C | not specified | Uncertain significance (Feb 12, 2024) | ||
| 19-7967704-G-A | not specified | Uncertain significance (Feb 23, 2025) | ||
| 19-7967796-C-T | Benign (Jul 25, 2018) | |||
| 19-7973763-C-T | not specified | Uncertain significance (Sep 23, 2023) | ||
| 19-7973772-C-T | not specified | Uncertain significance (Aug 27, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ELAVL1 | protein_coding | protein_coding | ENST00000407627 | 5 | 47081 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.988 | 0.0115 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.81 | 62 | 221 | 0.280 | 0.0000151 | 2164 |
| Missense in Polyphen | 9 | 54.206 | 0.16603 | 645 | ||
| Synonymous | 0.444 | 93 | 98.6 | 0.943 | 0.00000796 | 637 |
| Loss of Function | 3.40 | 0 | 13.5 | 0.00 | 7.54e-7 | 144 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding protein that binds to the 3'-UTR region of mRNAs and increases their stability (PubMed:14517288, PubMed:18285462). Involved in embryonic stem cells (ESCs) differentiation: preferentially binds mRNAs that are not methylated by N6-methyladenosine (m6A), stabilizing them, promoting ESCs differentiation (By similarity). Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs (PubMed:8626503, PubMed:17632515, PubMed:18285462, PubMed:23519412, PubMed:14731398). Binds avidly to the AU-rich element in FOS and IL3/interleukin-3 mRNAs. In the case of the FOS AU-rich element, binds to a core element of 27 nucleotides that contain AUUUA, AUUUUA, and AUUUUUA motifs. Binds preferentially to the 5'-UUUU[AG]UUU-3' motif in vitro (PubMed:8626503). With ZNF385A, binds the 3'-UTR of p53/TP53 mRNA to control their nuclear export induced by CDKN2A. Hence, may regulate p53/TP53 expression and mediate in part the CDKN2A anti-proliferative activity. May also bind with ZNF385A the CCNB1 mRNA (By similarity). Increases the stability of the leptin mRNA harboring an AU-rich element (ARE) in its 3' UTR (PubMed:29180010). {ECO:0000250|UniProtKB:P70372, ECO:0000269|PubMed:14517288, ECO:0000269|PubMed:14731398, ECO:0000269|PubMed:17632515, ECO:0000269|PubMed:18285462, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:23519412, ECO:0000269|PubMed:29180010, ECO:0000269|PubMed:8626503}.;
- Pathway
- AMPK signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;Endoderm Differentiation;Preimplantation Embryo;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Metabolism of RNA;mRNA Splicing - Major Pathway;HuR (ELAVL1) binds and stabilizes mRNA;Gastrin;Regulation of mRNA stability by proteins that bind AU-rich elements;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.493
Intolerance Scores
- loftool
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.415
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.720
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Elavl1
- Phenotype
- digestive/alimentary phenotype; limbs/digits/tail phenotype; immune system phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; hematopoietic system 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); normal 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); reproductive system phenotype; endocrine/exocrine gland phenotype; neoplasm; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- elavl1a
- Affected structure
- subintestinal vein
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;multicellular organism development;regulation of mRNA stability;positive regulation of translation;mRNA stabilization;protein homooligomerization;negative regulation of gene silencing by miRNA;3'-UTR-mediated mRNA stabilization;regulation of stem cell population maintenance
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;cytoplasmic stress granule;membrane;postsynapse;glutamatergic synapse;ribonucleoprotein complex
- Molecular function
- RNA binding;double-stranded RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;AU-rich element binding;protein kinase binding;miRNA binding;mRNA 3'-UTR AU-rich region binding;protein homodimerization activity