ELAVL3

ELAV like RNA binding protein 3, the group of RNA binding motif containing

Basic information

Region (hg38): 19:11451326-11481046

Links

ENSG00000196361 ∙ NCBI:1995 ∙ OMIM:603458 ∙ HGNC:3314 ∙ Uniprot:Q14576 ∙ 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 ELAVL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELAVL3 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					3	3
missense			9			9
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	3

Variants in ELAVL3

This is a list of pathogenic ClinVar variants found in the ELAVL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11454665-T-G		not specified	Uncertain significance (Oct 27, 2021)
19-11454744-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-11454776-C-T		not specified	Uncertain significance (Sep 22, 2023)
19-11454818-G-A		not specified	Uncertain significance (Aug 04, 2024)
19-11454837-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-11457129-T-C		not specified	Uncertain significance (Oct 11, 2024)
19-11458095-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-11458098-AG-A			Uncertain significance (Jun 30, 2023)
19-11458145-G-A		not specified	Uncertain significance (Oct 03, 2023)
19-11458582-G-A			Benign (Oct 20, 2021)
19-11466211-G-A			Benign (Jun 26, 2018)
19-11466644-T-C		not specified	Uncertain significance (Feb 15, 2023)
19-11466710-C-T		not specified	Uncertain significance (Jan 26, 2023)
19-11466783-G-A			Benign (Jun 26, 2018)
19-11466787-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-11466796-C-G		not specified	Likely benign (Jun 28, 2024)
19-11466797-C-G		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELAVL3	protein_coding	protein_coding	ENST00000359227	7	29721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.771	0.229	125736	0	3	125739	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.00	116	250	0.465	0.0000176	2389
Missense in Polyphen		11	85.361	0.12886		835
Synonymous	-0.953	127	114	1.11	0.00000969	754
Loss of Function	2.92	2	13.6	0.147	5.86e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000653	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to AU-rich sequences (AREs) of target mRNAs, including VEGF mRNA. May also bind poly-A tracts via RRM 3 (By similarity). May be involved in neuronal differentiation and maintenance. {ECO:0000250, ECO:0000269|PubMed:10710437}.

Recessive Scores

• pRec: 0.234

Intolerance Scores

• loftool: 0.334
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.390
• hipred: Y
• hipred_score: 0.789
• ghis: 0.727

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.704

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elavl3
• Phenotype: 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: elavl3
• Affected structure: hindbrain
• Phenotype tag: abnormal
• Phenotype quality: premature

Gene ontology

• Biological process: nervous system development;cell differentiation
• Molecular function: AU-rich element binding