ELAVL2

protein-coding

ELAV like RNA binding protein 2, the group of RNA binding motif containing

Gene summary

In humans, the ELAV like RNA binding protein gene family has four members (ELAVL1-4). ELAVL RNA binding proteins recognize AU-rich elements in the 3' UTRs of gene transcripts and thereby regulate gene expression post-transcriptionally. The protein encoded by this gene binds to several 3' UTRs, including its own and also that of FOS, ID, and POU5F1. This gene encodes ELAVL2 and, like ELAVL3 and ELAVL4, is expressed specifically in neurons and primarily localizes to the cytoplasm. This protein also forms a cytosolic complex with the normally nuclear-localized ELAVL1 protein. Alternative splicing of this gene results in multiple transcript variants encoding distinct protein isoforms. [provided by RefSeq, Jul 2020]

MANE transcript

NM_004432.5

Inheritance

—

ClinVar variants

U:49

Top phenotype

Global developmental delay

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr9:23,690,104-23,826,337

External References & Databases

Ensembl (ENSG00000107105)

Transcript & Mutation Effects

hg38 • Region Span ~136.2 kb

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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 ELAVL2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 8

Global developmental delayTotal: 1

ELAVL2-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004432.5. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			46 clinvar			46
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	0	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 130 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004432.5	RefSeq	NP_004423.2	6	MANE Select
ENST00000397312.7	Ensembl	ENSP00000380479.2	6	MANE Select
NM_001171195.2	RefSeq	NP_001164666.1	5	Standard
NM_001171197.2	RefSeq	NP_001164668.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

mRNA splicing, via spliceosome
regulation of transcription, DNA-templated

Molecular Function

RNA binding
mRNA 3'-UTR binding
protein binding

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397312
Coding exons: 6
Length: 136234
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125659
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.29	150	202	0.744	0.0000107	2362
Missense (PolyPhen)		22	63.38	0.34711		773
Synonymous	-2.73	102	72.4	1.41	0.00000403	702
Loss of Function	3.68	0	15.8	0.00	8.21e-7	183

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.;

Recessive Scores

pRec: 0.270

Intolerance Scores

RVIS EVS: -0.41
RVIS percentile EVS: 26.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.995

Gene Damage Prediction

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