ELAVL2

Summary

ELAVL2 (ELAV like RNA binding protein 2, HGNC:3313) is a protein-coding gene on chromosome 9p21.3, encoding ELAV-like protein 2 (Q12926). RNA-binding protein that binds to the 3’ untranslated region (3’UTR) of target mRNAs.

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.

Source: NCBI Gene 1993 — RefSeq curated summary.

At a glance

• GWAS associations: 35 (top 3% of genes corpus-wide)
• Clinical variants (ClinVar): 55 total
• Regional missense constraint (gnomAD): 1 of 3 regions constrained (≈4% of expected missense variation)
• GTEx eGene: eQTL in 11 tissues, sQTL in 0 (q < 0.05)
• Dosage sensitivity (ClinGen): haploinsufficiency little evidence, triplosensitivity no evidence
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.25 (highly constrained)
• MANE Select transcript: NM_004432
• Notable: 55 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3313
Approved symbol	ELAVL2
Name	ELAV like RNA binding protein 2
Location	9p21.3
Locus type	gene with protein product
Status	Approved
Aliases	HuB, HEL-N1
Ensembl gene	ENSG00000107105
Ensembl biotype	protein_coding
OMIM	601673
Entrez	1993

Gene structure

Transcript identifiers

Ensembl transcripts: 41 — 39 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

MANE Select: ENST00000397312

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 3: 3, TSL 5: 2

ENST00000397312, ENST00000223951, ENST00000380110, ENST00000380117, ENST00000423281, ENST00000440102, ENST00000462649, ENST00000544538, ENST00000886216, ENST00000886217, ENST00000886218, ENST00000886219, ENST00000886220, ENST00000886221, ENST00000886222, ENST00000886223, ENST00000886224, ENST00000886225, ENST00000886226, ENST00000886227, ENST00000921648, ENST00000921649, ENST00000921650, ENST00000921651, ENST00000921652, ENST00000921653, ENST00000921654, ENST00000921655, ENST00000921656, ENST00000921657, ENST00000921658, ENST00000921659, ENST00000921660, ENST00000921661, ENST00000921662, ENST00000921663, ENST00000955829, ENST00001086360, ENST00001112381, ENST00001112382, ENST00001141062

RefSeq mRNA: 41 — MANE Select: NM_004432 NM_001171195, NM_001171197, NM_001351455, NM_001351456, NM_001351457, NM_001351458, NM_001351459, NM_001351460, NM_001351461, NM_001351462, NM_001351463, NM_001351464, NM_001351465, NM_001351466, NM_001351467, NM_001351468, NM_001351469, NM_001351470, NM_001351471, NM_001351472, NM_001351473, NM_001351474, NM_001351475, NM_001351476, NM_001351477, NM_001351478, NM_001385693, NM_001385694, NM_001385695, NM_001385696, NM_001385697, NM_001385698, NM_001385699, NM_001385700, NM_001385701, NM_001385702, NM_001385703, NM_001385704, NM_001385705, NM_001385707, NM_004432

CCDS: CCDS55298, CCDS6515, CCDS87645

Canonical transcript exons

ENST00000397312 — 7 exons

Exon	Start	End
ENSE00001528157	23825806	23826240
ENSE00003517233	23731022	23731125
ENSE00003888758	23704918	23705071
ENSE00003891748	23762006	23762249
ENSE00003892764	23693448	23693486
ENSE00003894202	23701379	23701604
ENSE00003895823	23690104	23692884

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 98.75.

FANTOM5 (CAGE): breadth broad, TPM avg 9.3693 / max 348.0820, expressed in 538 samples.

Highest expression (Bgee): Brodmann (1909) area 23, substantia nigra pars compacta, substantia nigra pars reticulata, middle temporal gyrus, lateral nuclear group of thalamus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ELAVL2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 11 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

11 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Esophagus Muscularis	eqtl	4.3e-08	+0.34	9:23583600:G:A
Thyroid	eqtl	1.8e-06	+0.43	9:23817247:T:TA
Adipose Subcutaneous	eqtl	5.1e-06	+0.28	9:23830405:A:G
Breast Mammary Tissue	eqtl	3.3e-05	+0.29	9:23829730:T:G
Stomach	eqtl	7.4e-05	+0.53	9:23819942:C:T
Nerve Tibial	eqtl	4.6e-04	+0.27	9:23830217:C:G
Brain Caudate basal ganglia	eqtl	7.0e-03	-0.20	9:23424338:A:G
Adipose Visceral Omentum	eqtl	2.3e-02	+0.26	9:23817247:T:TA
Brain Cerebellar Hemisphere	eqtl	3.2e-02	-0.25	9:22919246:T:C
Colon Transverse	eqtl	3.5e-02	+0.44	9:23378256:C:G
Brain Cortex	eqtl	3.7e-02	+0.09	9:24514392:T:G

FANTOM5 promoters

showing 10 of 14 alternative TSS:

Promoter ID	TPM avg	Samples expressed
100296	2.4550	334
100290	2.1255	419
100295	2.0622	266
100294	1.2349	225
100293	0.3651	116
100297	0.3387	157
100289	0.2151	64
100300	0.1678	100
100291	0.1314	77
100299	0.1166	74

Top tissues by expression

showing 100 of 282 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	98.75	gold quality
substantia nigra pars compacta	UBERON:0001965	98.72	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.69	gold quality
middle temporal gyrus	UBERON:0002771	98.12	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.81	gold quality
ganglionic eminence	UBERON:0004023	97.57	gold quality
endothelial cell	CL:0000115	97.24	gold quality
cortical plate	UBERON:0005343	96.85	gold quality
pons	UBERON:0000988	96.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	96.44	gold quality
postcentral gyrus	UBERON:0002581	96.44	gold quality
parietal lobe	UBERON:0001872	96.36	gold quality
superior vestibular nucleus	UBERON:0007227	96.31	gold quality
superior frontal gyrus	UBERON:0002661	95.38	gold quality
secondary oocyte	CL:0000655	95.04	gold quality
dorsal root ganglion	UBERON:0000044	94.90	gold quality
entorhinal cortex	UBERON:0002728	94.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.62	gold quality
buccal mucosa cell	CL:0002336	93.40	silver quality
primary visual cortex	UBERON:0002436	93.38	gold quality
ventral tegmental area	UBERON:0002691	93.16	gold quality
occipital lobe	UBERON:0002021	92.39	gold quality
frontal pole	UBERON:0002795	91.26	gold quality
cerebellar vermis	UBERON:0004720	91.09	gold quality
sperm	CL:0000019	90.96	gold quality
prefrontal cortex	UBERON:0000451	90.83	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.97	gold quality
oocyte	CL:0000023	89.57	gold quality
frontal cortex	UBERON:0001870	89.03	gold quality
neocortex	UBERON:0001950	89.01	gold quality
cerebral cortex	UBERON:0000956	88.20	gold quality
trigeminal ganglion	UBERON:0001675	88.02	gold quality
adult organism	UBERON:0007023	88.00	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.89	gold quality
anterior cingulate cortex	UBERON:0009835	87.69	gold quality
cingulate cortex	UBERON:0003027	87.64	gold quality
male germ cell	CL:0000015	87.44	gold quality
lateral globus pallidus	UBERON:0002476	86.63	gold quality
ventricular zone	UBERON:0003053	85.99	gold quality
hypothalamus	UBERON:0001898	85.72	gold quality
paraflocculus	UBERON:0005351	85.16	gold quality
temporal lobe	UBERON:0001871	84.99	gold quality
testis	UBERON:0000473	83.90	gold quality
embryo	UBERON:0000922	83.78	gold quality
midbrain	UBERON:0001891	83.53	gold quality
right frontal lobe	UBERON:0002810	83.42	gold quality
telencephalon	UBERON:0001893	83.41	gold quality
substantia nigra	UBERON:0002038	82.36	gold quality
medulla oblongata	UBERON:0001896	82.21	gold quality
right testis	UBERON:0004534	82.21	gold quality
cerebellum	UBERON:0002037	82.15	gold quality
brain	UBERON:0000955	81.70	gold quality
cerebellar cortex	UBERON:0002129	81.68	gold quality
left testis	UBERON:0004533	81.52	gold quality
cerebellar hemisphere	UBERON:0002245	81.43	gold quality
forebrain	UBERON:0001890	81.37	gold quality
central nervous system	UBERON:0001017	81.20	gold quality
Ammon’s horn	UBERON:0001954	80.93	gold quality
palpebral conjunctiva	UBERON:0001812	80.14	gold quality
dorsal plus ventral thalamus	UBERON:0001897	79.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.86	gold quality
amygdala	UBERON:0001876	78.58	gold quality
eye	UBERON:0000970	76.94	gold quality
Brodmann (1909) area 46	UBERON:0006483	74.81	silver quality
Brodmann (1909) area 10	UBERON:0013541	74.44	gold quality
adrenal tissue	UBERON:0018303	73.53	gold quality
caudate nucleus	UBERON:0001873	73.30	gold quality
globus pallidus	UBERON:0001875	72.61	gold quality
putamen	UBERON:0001874	70.81	gold quality
nucleus accumbens	UBERON:0001882	70.41	gold quality
medial globus pallidus	UBERON:0002477	70.35	gold quality
middle frontal gyrus	UBERON:0002702	69.15	gold quality
endometrium epithelium	UBERON:0004811	68.72	gold quality
pigmented layer of retina	UBERON:0001782	67.27	gold quality
retina	UBERON:0000966	67.26	gold quality
subthalamic nucleus	UBERON:0001906	67.13	gold quality
corpus callosum	UBERON:0002336	66.91	gold quality
inferior vagus X ganglion	UBERON:0005363	66.56	gold quality
spinal cord	UBERON:0002240	65.66	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	65.19	gold quality
hair follicle	UBERON:0002073	62.03	gold quality
lower lobe of lung	UBERON:0008949	58.81	silver quality
colonic epithelium	UBERON:0000397	58.29	silver quality
calcaneal tendon	UBERON:0003701	57.71	gold quality
tibialis anterior	UBERON:0001385	57.63	silver quality
diaphragm	UBERON:0001103	57.06	gold quality
ovary	UBERON:0000992	55.84	gold quality
adenohypophysis	UBERON:0002196	55.81	gold quality
upper leg skin	UBERON:0004262	55.71	gold quality
pituitary gland	UBERON:0000007	55.53	gold quality
rectum	UBERON:0001052	55.20	gold quality
deltoid	UBERON:0001476	54.42	silver quality
germinal epithelium of ovary	UBERON:0001304	54.06	gold quality
thymus	UBERON:0002370	53.57	gold quality
right adrenal gland cortex	UBERON:0035827	52.76	gold quality
tendon	UBERON:0000043	52.72	gold quality
mucosa of transverse colon	UBERON:0004991	52.21	gold quality
ileal mucosa	UBERON:0000331	52.13	silver quality
right adrenal gland	UBERON:0001233	52.06	gold quality
right ovary	UBERON:0002118	51.72	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	1337.58
E-GEOD-124263	yes	609.39
E-GEOD-134144	yes	534.50
E-MTAB-11121	yes	428.26
E-HCAD-35	yes	70.06
E-HCAD-25	yes	39.80
E-HCAD-5	yes	26.90
E-ANND-3	yes	5.38

HPA expression

RNA tissue specificity: Group enriched

showing 60 of 72 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Postcentral gyrus	tissue	99.5
Pons	tissue	75.3
Locus coeruleus	tissue	55.7
Thalamus	tissue	49.0
Cerebral cortex	tissue	47.7	high
Occipital cortex	tissue	47.7
Somatosensory cortex	tissue	44.9
Substantia nigra	tissue	44.2
Superior colliculi	tissue	44.0
Frontal cortex	tissue	41.7
Retrosplenial and cingulate cortex	tissue	41.2
Hippocampal formation	tissue	40.7
Testis	tissue	40.3	high
Prefrontal cortex	tissue	40.0
Motor cortex	tissue	40.0
Midbrain	tissue	40.0
Retrosplenial cortex	tissue	39.1
Entorhinal cortex	tissue	37.4
Hypothalamus	tissue	36.9
Medulla oblongata	tissue	36.4
Cerebellum	tissue	36.0	high
Periaqueductal gray	tissue	34.5
Insular cortex	tissue	32.6
Temporal cortex	tissue	31.1
Ventral forebrain	tissue	30.9
Hippocampus	tissue	27.7	medium
Caudate putamen	tissue	26.7
Spinal cord	tissue	26.1
Amygdala	tissue	25.8
Septum	tissue	25.6
Putamen	tissue	19.7
Olfactory bulb	tissue	17.0
Basal ganglia	tissue	13.6	medium
Nucleus accumbens	tissue	12.4
Corpus callosum	tissue	7.4
Choroid plexus	tissue	6.6
Retina	tissue	4.6
Ovary	tissue	1.9	low
Adrenal gland	tissue	1.2	not detected
Pituitary gland	tissue	0.9
Endometrium 1	tissue	0.5	not detected
Skin 1	tissue	0.4	not detected
Rectum	tissue	0.4	low
Urinary bladder	tissue	0.4	not detected
Epididymis	tissue	0.4	not detected
Kidney	tissue	0.4	high
Bone marrow	tissue	0.4	not detected
Colon	tissue	0.3	low
Thyroid gland	tissue	0.3	not detected
Prostate	tissue	0.3	low
Breast	tissue	0.2	not detected
Esophagus	tissue	0.2	not detected
Smooth muscle	tissue	0.2	not detected
Lung	tissue	0.2	not detected
Small intestine	tissue	0.2	low
Gallbladder	tissue	0.2	not detected
Cervix	tissue	0.1	not detected
Lymph node	tissue	0.1	not detected
Stomach 1	tissue	0.1	low
Heart muscle	tissue	0.1	not detected

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Lateral hypothalamic area (82.2), Paracentral lobule, anterior (63.8), Nucleus raphe magnus (63.2), Olfactory tubercle (63.1), Habenula (62.5).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EOMES, TBX21

miRNA regulators (miRDB)

Targeting ELAVL2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 289 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-340-5P	100.00	72.50	4437
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.249, missense Z 0.562 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000397312 splits into 3 regions with different missense tolerance; 1 is missense-constrained (≈4% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
9:23,692,560–23,705,054	295 / 306.1	0.96	no
9:23,705,055–23,731,048	5 / 18.4	0.27	yes (p 1.7e-03)
9:23,731,049–23,762,234	132 / 118.3	1.12	no
ClinGen dosage: haploinsufficiency 1 (little evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 11)

• the mutually antagonistic action of two RNA-binding proteins, Hu and hnRNP K, control the timing of the switch from proliferation to neuronal differentiation through the post-transcriptional regulation of p21 mRNA (PMID:15671036)
• increased level of mRNA transcripts detected in Small Cell Lung Cancer patients (PMID:18607064)
• Tests for gene-environment interaction between these 33 genes and maternal smoking found evidence for interaction with two additional genes: GRID2 and ELAVL2 among European mothers (PMID:23512105)
• ELAVL2-regulated co-expression networks are also enriched for neurodevelopmental and synaptic genes, and include genes with human-specific patterns of expression in the frontal pole. Together, these data suggest that ELAVL2 regulation of transcript expression is critical for neuronal function and clinically relevant to autism (PMID:27260404)
• HuB plays a major role in the activation of proto-oncogenes. (PMID:31358321)
• Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective. (PMID:32599245)
• HuB and HuD repress telomerase activity by dissociating HuR from TERC. (PMID:33589924)
• Bioinformatic Analysis Identified Hub Genes Associated with Heterocyclic Amines Induced Cytotoxicity of Peripheral Blood Mononuclear Cells. (PMID:34946837)
• Identification of Hub Genes of Lung Adenocarcinoma Based on Weighted Gene Co-Expression Network in Chinese Population. (PMID:36032660)
• Identification of Hub Genes Associated with Resistance to Prednisolone in Acute Lymphoblastic Leukemia Based on Weighted Gene Co-expression Network Analysis. (PMID:36877306)
• Analysis of Enrichment Pathway, Hub Gene, and Protein-Protein Interaction Network in Rheumatoid Arthritis and Construction of Molecular Subtypes in Peripheral Blood. (PMID:37773661)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	elavl2	ENSDARG00000040732
mus_musculus	Elavl2	ENSMUSG00000008489
rattus_norvegicus	Elavl2	ENSRNOG00000006853
drosophila_melanogaster	Rbp9	FBGN0010263
drosophila_melanogaster	fne	FBGN0086675

Paralogs (24): ELAVL1 (ENSG00000066044), PABPC1 (ENSG00000070756), RBMS2 (ENSG00000076067), PABPC4 (ENSG00000090621), PABPC1L (ENSG00000101104), RBM24 (ENSG00000112183), TARDBP (ENSG00000120948), HNRNPR (ENSG00000125944), RBM38 (ENSG00000132819), SYNCRIP (ENSG00000135316), SF3B4 (ENSG00000143368), RBMS3 (ENSG00000144642), PABPC3 (ENSG00000151846), RBMS1 (ENSG00000153250), RBM45 (ENSG00000155636), ELAVL4 (ENSG00000162374), PABPC5 (ENSG00000174740), PUF60 (ENSG00000179950), PABPC1L2B (ENSG00000184388), PABPC1L2A (ENSG00000186288), RBM34 (ENSG00000188739), ELAVL3 (ENSG00000196361), RBM14 (ENSG00000239306), PABPC4L (ENSG00000254535)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1100887) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 11 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal ovary morphology	1
small ovary	1
irregularly shaped pupil	1
postnatal growth retardation	1
female infertility	1
absent oocytes	1
decreased survivor rate	1
oocyte degeneration	1
postnatal lethality, incomplete penetrance	1
preweaning lethality, complete penetrance	1
absent primordial ovarian follicles	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Drosophila virilis	P23241	100.0%	Diamond
Pongo abelii	Q5NVC8	100.0%	Diamond
Xenopus tropicalis	A4QNI8	99.8%	Diamond
Xenopus laevis	Q7SZT7	99.8%	Diamond
Gallus gallus	Q7T2T1	99.8%	Diamond
Drosophila erecta	B3NGA1	99.5%	Diamond
Drosophila yakuba	B4PIS2	99.5%	Diamond
Oryza sativa Indica Group	B8BCZ8	99.5%	Diamond
Oryza sativa Japonica Group	Q6K271	99.5%	Diamond
Drosophila sechellia	B4HUE4	98.6%	Diamond
Drosophila simulans	B4QRJ0	98.6%	Diamond
Bos taurus	Q3ZBP3	98.0%	Diamond
Drosophila grimshawi	B4IX08	97.6%	Diamond
Drosophila mojavensis	B4KX02	96.3%	Diamond
Drosophila ananassae	B3M3R5	92.1%	Diamond
Triticum aestivum	Q2QKB4	90.8%	Diamond
Musca domestica	O17310	90.6%	Diamond
Chrysomya rufifacies	O97018	90.6%	Diamond
Caenorhabditis briggsae	A8WLV5	90.1%	Diamond
Drosophila willistoni	B4MM23	90.1%	Diamond
Caenorhabditis elegans	Q19706	90.1%	Diamond
Nicotiana plumbaginifolia	Q9ZR39	89.8%	Diamond
Drosophila subobscura	Q24668	89.1%	Diamond
Arabidopsis thaliana	Q9FIU6	85.7%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
IZUMO3	protein-coding	100129669

Protein

Protein identifiers

ELAV-like protein 2 — Q12926 (reviewed: Q12926)

Alternative names: ELAV-like neuronal protein 1, Hu-antigen B, Nervous system-specific RNA-binding protein Hel-N1

All UniProt accessions (4): A0A0A0MRX1, B1AM48, C9JB16, Q12926

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein that binds to the 3’ untranslated region (3’UTR) of target mRNAs. Seems to recognize a GAAA motif. Can bind to its own 3’UTR, the FOS 3’UTR and the ID 3’UTR.

Subunit / interactions. Interacts with IGF2BP1. Interacts with MAP1B light chain LC1.

Tissue specificity. Brain; neural-specific.

Similarity. Belongs to the RRM elav family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q12926-1	1	yes
Q12926-2	2

RefSeq proteins (41): NP_001164666, NP_001164668, NP_001338384, NP_001338385, NP_001338386, NP_001338387, NP_001338388, NP_001338389, NP_001338390, NP_001338391, NP_001338392, NP_001338393, NP_001338394, NP_001338395, NP_001338396, NP_001338397, NP_001338398, NP_001338399, NP_001338400, NP_001338401, NP_001338402, NP_001338403, NP_001338404, NP_001338405, NP_001338406, NP_001338407, NP_001372622, NP_001372623, NP_001372624, NP_001372625, NP_001372626, NP_001372627, NP_001372628, NP_001372629, NP_001372630, NP_001372631, NP_001372632, NP_001372633, NP_001372634, NP_001372636, NP_004423* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR002343	Hud_Sxl_RNA	Family
IPR006548	ELAD_HU_SF	Family
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034914	HuB_RRM3	Domain
IPR034999	HuB_RRM2	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (8 total): domain 3, chain 1, region of interest 1, modified residue 1, splice variant 1, sequence conflict 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q12926-F1	75.93	0.48

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm; cytosol

Antibody reliability (HPA): IH enhanced · IF approved

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1)

Type	Positions
Phosphoserine	221

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 1; 1 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

1 pathways:

ID	Pathway	Evidence
R-HSA-9918481	Dengue Virus-Host Interactions ⚕	curated

MSigDB gene sets: 367 (showing top): AHRARNT_01, AP1_01, YAATNRNNNYNATT_UNKNOWN, MORF_FLT1, BENPORATH_ES_WITH_H3K27ME3, MORF_MSH3, NKX25_02, GCANCTGNY_MYOD_Q6, MORF_BRCA1, RACCACAR_AML_Q6, MORF_ESR1, MODULE_16, FOXO1_01, GGGTGGRR_PAX4_03, GTACAGG_MIR486

GO Biological Process (2): regulation of DNA-templated transcription (GO:0006355), negative regulation of mRNA processing (GO:0050686)

GO Molecular Function (5): RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), protein-RNA adaptor activity (GO:0140517), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (2): ribonucleoprotein complex (GO:1990904), nucleus (GO:0005634)

Reactome top-level categories

1 top-level categories:

Category	Pathways
Dengue Virus Infection	1

GO top-level categories

12 GO namespaces:

Category	Terms
binding	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
mRNA processing	1
regulation of mRNA processing	1
negative regulation of mRNA metabolic process	1
nucleic acid binding	1
mRNA binding	1
protein-macromolecule adaptor activity	1
protein-containing complex	1
intracellular membrane-bounded organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 9 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
RNA binding	MF	high-throughput assay

Protein interactions and networks

STRING

showing 16 of 1,158 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ELAVL2	RBFOX1	Q9NWB1	526
ELAVL2	IFNA7	P01567	480
ELAVL2	IFNA16	P05015	478
ELAVL2	IFNA21	P01568	471
ELAVL2	IFNA8	P01565	465
ELAVL2	IFNA5	P01569	460
ELAVL2	MYCN	P04198	453
ELAVL2	KHSRP	Q92945	453
ELAVL2	NOVA1	P51513	451
ELAVL2	IFNA6	P05013	440
ELAVL2	IFNA4	P05014	438
ELAVL2	IFNA14	P01570	435
ELAVL2	IFNA10	P01566	429
ELAVL2	RBFOX2	O43251	428
ELAVL2	FMR1	Q06787	423
ELAVL2	CACNB4	O00305	423

IntAct

Human interaction partners of ELAVL2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

11 partners by confidence:

Partner	Interaction type	MIscore	Records
CASC3	association	0.530	1
IGF2BP3	association	0.530	1
LIN28B	association	0.530	1
DYRK1A	physical association	0.500	1
HNRNPAB	physical association	0.370	1
HOXC9	physical association	0.370	1
NR2E3	physical association	0.370	1
RBFOX2	physical association	0.370	1
GAPDHS	association	0.350	1
SHANK3	association	0.350	1
ZC3H11A	association	0.350	1

BioGRID (287 interactions; top human partners by supporting records): DYRK1A (Affinity Capture-MS; 3 records), ELAVL3 (Affinity Capture-MS; 3 records), HIST1H1A (Affinity Capture-MS; 3 records), IGF2BP2 (Affinity Capture-MS; 3 records), ILF2 (Affinity Capture-MS; 3 records), RBMX (Affinity Capture-MS; 3 records), TRA2A (Affinity Capture-MS; 3 records), ACIN1 (Affinity Capture-MS; 2 records), ALG13 (Affinity Capture-MS; 2 records), APOBEC3B (Affinity Capture-MS; 2 records), APOBEC3D (Affinity Capture-MS; 2 records), APOBEC3F (Affinity Capture-MS; 2 records), AQR (Affinity Capture-MS; 2 records), ATXN2 (Affinity Capture-MS; 2 records), CASC3 (Affinity Capture-MS; 2 records)

SIGNOR signaling

1 signaling interactions:

A	Effect	B	Mechanism
ELAVL2	“up-regulates quantity”	ADAM10	“post transcriptional regulation”

Disease & clinical

Genetic variants

Variant evidence for ELAVL2: 55 ClinVar records (0 pathogenic / likely pathogenic); 35 GWAS associations.

ClinVar

55 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	0
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 39 predictions of 1,134):

Position(s)	Effect	Δscore	Sites
9:23693334	acceptor_gain	1.0000
9:23704916–23704917	donor_loss	1.0000	5
9:23705072–23705073	acceptor_loss	1.0000	5
9:23731020–23731021	donor_loss	1.0000	4
9:23731126–23731127	acceptor_loss	1.0000	6
9:23731129	acceptor_gain	1.0000
9:23762004–23762005	donor_loss	1.0000	5
9:23762250–23762251	acceptor_loss	1.0000	6
9:23762258	acceptor_gain	1.0000
9:23701377–23701378	donor_loss	0.9900	5

HPA cancer prognostics

RNA cancer specificity: Cancer enhanced (Kidney Chromophobe, Testicular Germ Cell Tumor)

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Glioblastoma Multiforme (validation)	favorable	0.000376

Disease associations

OMIM: gene MIM:601673 | disease phenotypes:

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (6 panels, 0 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

6 panels:

Panel	Rating
Early onset or syndromic epilepsy	amber
Hypotonic infant	amber
Intellectual disability	amber
Leukodystrophy, childhood onset	amber
Paediatric disorders	amber
Unexplained death in infancy and sudden unexplained death in childhood	amber

GWAS associations

showing 30 of 35 associations:

Study	Trait	p-value
GCST007800_52	Asthma (childhood onset)	3e-16
GCST006940_119	Neurociticism	9e-13
GCST007692_88	Chronic obstructive pulmonary disease	4e-12
GCST006940_55	Neurociticism	8e-12
GCST006945_18	Feeling guilty	4e-11
GCST006269_1107	General cognitive ability	1e-10
GCST012114_11	Sociability score	5e-10
GCST012490_111	Femur bone mineral density x serum urate levels interaction	7e-10
GCST011768_8	Schizophrenia	2e-9
GCST006269_316	General cognitive ability	3e-9
GCST006482_3	Lung function (FEV1/FVC)	3e-9
GCST005316_353	Intelligence (MTAG)	4e-9
GCST011769_13	Schizophrenia	5e-9
GCST007387_29	Insomnia symptoms (never/rarely vs. sometimes/usually)	7e-9
GCST005835_4	Remission after SSRI treatment in MDD or neuroticism	1e-8
GCST006269_268	General cognitive ability	2e-8
GCST003447_7	Neuroticism	3e-8
GCST003770_42	Neuroticism	3e-8
GCST004558_160	Body mass index (joint analysis main effects and physical activity interaction)	4e-8
GCST90014325_15	Asthma	5e-8
GCST007798_153	Asthma	8e-8
GCST004560_1	Body mass index in physically inactive individuals	1e-7
GCST007388_45	Insomnia symptoms (never/rarely vs. usually)	2e-7
GCST004557_159	Body mass index	3e-7
GCST007797_48	Asthma onset (childhood vs adult)	3e-7
GCST012354_5	Anxiety	3e-7
GCST005232_65	Neuroticism	4e-7
GCST012354_6	Anxiety	5e-7
GCST006496_4	Glomerular filtration rate change in heart transplantation	2e-6
GCST007433_5	Fulminant type 1 diabetes	5e-6

EFO canonical traits (from GWAS)

17 canonical traits:

EFO ID	Trait name
EFO:0007660	neuroticism measurement
EFO:0004760	t-tau measurement
EFO:0004340	body mass index
EFO:0008002	physical activity measurement
EFO:0004337	intelligence
EFO:0005658	response to selective serotonin reuptake inhibitor
EFO:0004713	FEV/FVC ratio
EFO:0006829	GFR change measurement
EFO:0007043	response to transplant
EFO:0009595	guilt measurement
EFO:0007876	insomnia measurement
EFO:0004847	age at onset
EFO:0004338	body weight
EFO:0005937	longitudinal BMI measurement
EFO:0009592	social interaction measurement
EFO:0009863	anxiety measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

PharmGKB variant annotations

Per-publication pharmacogenomic findings for this gene (significant associations).

1 published findings:

Variant	Drug(s)	Category	Finding	PMID
rs73482673	clozapine	Toxicity	Allele A is associated with increased likelihood of Neutropenia when treated with clozapine in people with Schizophrenia as compared to allele G.	PMID:34083506

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects splicing, increases abundance, affects cotreatment, decreases expression	3
Valproic Acid	affects expression, decreases expression, decreases methylation, increases expression	3
potassium chromate(VI)	affects cotreatment, decreases expression, increases expression	2
Aflatoxin B1	increases methylation, decreases methylation	2
Particulate Matter	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
geraniol	decreases expression	1
trichostatin A	decreases expression	1
arsenite	increases methylation	1
benzo(e)pyrene	increases methylation	1
hydroquinone	decreases degradation, decreases expression, increases reaction	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
chromium hexavalent ion	affects expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	decreases expression	1
abrine	increases expression	1
incobotulinumtoxinA	decreases expression	1
NSC 689534	affects binding, decreases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects splicing, increases abundance, affects cotreatment	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Copper	affects binding, decreases expression	1
Lead	affects splicing	1
Methapyrilene	increases methylation	1
Oxygen	increases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Thiram	increases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.