ELP4 (elongator acetyltransferase complex subunit 4)

Gene

• Entrez ID: 26610
• Gene name: Elongator acetyltransferase complex subunit 4
• Gene symbol: ELP4
• Synonyms (NCBI Gene): AN, AN2, C11orf19, PAX6NEB, PAXNEB, dJ68P15A.1, hELP4
• Chromosome: 11
• Chromosome location: 11p13
• Summary: This gene encodes a component of the six subunit elongator complex, a histone acetyltransferase complex that associates directly with RNA polymerase II during transcriptional elongation. The human gene can partially complement sensitivity phenotypes of ye

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs606231388	C>A	Pathogenic	Intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT440726	ebv-miR-BART7-3p	HITS-CLIP	22473208
MIRT440726	ebv-miR-BART7-3p	HITS-CLIP	22473208
MIRT961682	hsa-miR-1305	CLIP-seq
MIRT961683	hsa-miR-1914	CLIP-seq
MIRT961684	hsa-miR-3173-3p	CLIP-seq
MIRT961685	hsa-miR-4428	CLIP-seq
MIRT961686	hsa-miR-4521	CLIP-seq
MIRT961687	hsa-miR-498	CLIP-seq
MIRT961682	hsa-miR-1305	CLIP-seq
MIRT961683	hsa-miR-1914	CLIP-seq
MIRT961687	hsa-miR-498	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002098	Process	TRNA wobble uridine modification	IBA
GO:0002098	Process	TRNA wobble uridine modification	IEA
GO:0002098	Process	TRNA wobble uridine modification	NAS	27847465
GO:0005515	Function	Protein binding	IPI	17577209, 22854966, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	11818576, 22854966
GO:0005737	Component	Cytoplasm	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IDA	11818576
GO:0006417	Process	Regulation of translation	NAS	22854966
GO:0008023	Component	Transcription elongation factor complex	IDA	11818576
GO:0008033	Process	TRNA processing	IEA
GO:0008607	Function	Phosphorylase kinase regulator activity	IDA	11818576
GO:0033588	Component	Elongator holoenzyme complex	IBA
GO:0033588	Component	Elongator holoenzyme complex	IDA	22854966
GO:0033588	Component	Elongator holoenzyme complex	IEA
GO:0033588	Component	Elongator holoenzyme complex	IPI	22854966

Other IDs

• MIM: 606985
• HGNC: 1171
• e!Ensembl: ENSG00000109911

Protein

• UniProt ID: Q96EB1
• Protein name: Elongator complex protein 4 (hELP4) (PAX6 neighbor gene protein)
• Protein function: Component of the elongator complex which is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine) (PubMed:29332244). Th
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05625	PAXNEB	45 → 415	PAXNEB protein	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:11889558}.
• Sequence:

  MAAVATCGSVAASTGSAVATASKSNVTSFQRRGPRASVTNDSGPRLVSIAGTRPSVRNGQ
  LLVSTGLPALDQLLGGGLAVGTVLLIEEDKYNIYSPLLFKYFLAEGIVNGHTLLVASAKE
  DPANILQELPAPLLDDKCKKEFDEDVYNHKTPESNIKMKIAWRYQLLPKMEIGPVSSSRF
  GHYYDASKRMPQELIEASNWHGFFLPEKISSTLKVEPCSLTPGYTKLLQFIQNIIYEEGF
  DGSNPQKKQRNILRIGIQNLGSPLWGDDICCAENGGNSHSLTKFLYVLRGLLRTSLSACI
  ITMPTHLIQNKAIIARVTTLSDVVVGLESFIGSERETNPLYKDYHGLIHIRQIPRLNNLI
  CDESDVKDLAFKLKRKLFTIERLHLPPDLSDTVSRSSKMDLAESAKRLGPGCGMMAGGKK
  HLDF

• Sequence length: 424

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Aniridia 1	Pathogenic	rs606231388	RCV000106409	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cognitive impairment	Likely pathogenic	rs755762601, rs758883150	RCV001797564 RCV001797565	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic	rs755762601, rs758883150	RCV001797564 RCV001797565	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Seizure	Likely pathogenic	rs755762601, rs758883150	RCV001797564 RCV001797565	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANIRIDIA	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia 2	Uncertain significance; Benign	ClinVar ClinVar, GWAS catalog, HPO ClinVar, GWAS catalog, HPO	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
ANIRIDIA TYPE 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANIRIDIA TYPE 2	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANOPHTHALMIA-MICROPHTHALMIA SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANOPHTHALMOS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism spectrum disorder	Likely benign; association	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOBOMA OF OPTIC DISC	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL OCULAR COLOBOMA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ELP4-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROINTESTINAL STROMAL TUMORS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IRIDO-CORNEO-TRABECULAR DYSGENESIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KERATITIS, HEREDITARY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACULAR TELANGIECTASIA TYPE 2	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NYSTAGMUS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR DYSGENESIS CAUSED BY DEFECTS IN PAX6 REGULATION	—	ClinGen, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WAGR SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Aniridia	Aniridia	BEFREE	11889558, 2347591, 28598868		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia	Aniridia	Pubtator	21364908, 2544995, 7688557	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia	Aniridia	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia	Aniridia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia	Aniridia	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia type 1	Aniridia	CLINVAR_DG	11309364, 12552561, 27431685, 28321846, 29618921		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia type 2	Aniridia	BEFREE	2347591		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aniridia type 2	Aniridia	GENOMICS_ENGLAND_DG	24290376, 29217025		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANTERIOR SEGMENT DYSGENESIS 5	Anterior segment dysgenesis	CLINVAR_DG	11309364, 12552561, 27431685, 28321846, 29618921		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	GWASCAT_DG	29942085		★☆☆☆☆ Found in Text Mining only
Arachnoid Cysts	Arachnoid cysts	Pubtator	31743616	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	26010655		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Benign Rolandic Epilepsy	Benign Rolandic Epilepsy	BEFREE	25301525		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
CNS disorder	CNS Disorder	BEFREE	28167615		★☆☆☆☆ Found in Text Mining only
Coloboma of optic disc	Coloboma of optic disc	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Depressive Disorder	Major depressive disorder	Pubtator	31743616	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	19172991	Associate	★☆☆☆☆ Found in Text Mining only
Dysautonomia, Familial	Dysautonomia	BEFREE	28167615		★☆☆☆☆ Found in Text Mining only
Epilepsies Partial	Partial epilepsy	Pubtator	19172991, 19682046	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsies, Partial	Epilepsy	BEFREE	19172991, 19682046, 22818593		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	26010655		★☆☆☆☆ Found in Text Mining only
Epilepsy Rolandic	Rolandic epilepsy	Pubtator	19172991, 20424645	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy, Rolandic	Epilepsy	BEFREE	19172991, 20424645, 20825490, 24995671		★☆☆☆☆ Found in Text Mining only
FOVEAL HYPOPLASIA 1	Foveal hypoplasia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Sarcoma	Gastrointestinal stromal tumor	CTD_human_DG	27793025		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Tumors	Gastrointestinal stromal tumor	CTD_human_DG	27793025		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glaucoma	Glaucoma	GWASCAT_DG	25027321		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	BEFREE	2347591, 26010655		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	2544995	Associate	★☆☆☆☆ Found in Text Mining only
Keratitis, hereditary	Keratitis, Hereditary	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Language Disorders	Language Disorders	BEFREE	26010655		★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	2347591, 26010655		★☆☆☆☆ Found in Text Mining only
Nephroblastoma	Nephroblastoma	BEFREE	2347591		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	19172991		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	Pubtator	26449484	Associate	★☆☆☆☆ Found in Text Mining only
Optic Nerve Hypoplasia, Bilateral	Optic nerve hypoplasia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	31784339		★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	19172991	Associate	★☆☆☆☆ Found in Text Mining only
WAGR Syndrome	WAGR Syndrome	BEFREE	2347591		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WAGR Syndrome	WAGR Syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Wilms Tumor	Wilms tumor	Pubtator	7688557	Associate	★☆☆☆☆ Found in Text Mining only