ELP4

elongator acetyltransferase complex subunit 4, the group of Elongator acetyltransferase complex

Basic information

Region (hg38): 11:31509754-31790324

Previous symbols: [ "C11orf19" ]

Links

ENSG00000109911 ∙ NCBI:26610 ∙ OMIM:606985 ∙ HGNC:1171 ∙ Uniprot:Q96EB1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• aniridia 2 (Limited), mode of inheritance: AD
• aniridia 2 (Strong), mode of inheritance: AD
• aniridia 1 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Aniridia 2	AD	Ophthalmologic; Pharmacogenomic	Individuals with PAX6 related eye anomalies (including due to cis-regulatory variants in ELP4) may be recognizable, but some may also be at high risk of developing glaucoma; Agents that may contribute to glaucoma should be avoided	Ophthalmologic	24290376
The condition has been reported as caused by an intronic variant in a PAX6 cis-regulatory element

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELP4 gene.

• Foveal hypoplasia 1 (95 variants)
• Autosomal dominant keratitis (95 variants)
• Anophthalmia-microphthalmia syndrome (84 variants)
• carboxymethyl-dextran-A2-gadolinium-DOTA (84 variants)
• 11p partial monosomy syndrome (71 variants)
• Aniridia, Cerebellar Ataxia, And Intellectual Disability (62 variants)
• not provided (52 variants)
• Congenital aniridia (48 variants)
• Aniridia 1 (33 variants)
• Irido-corneo-trabecular dysgenesis (11 variants)
• Anophthalmia (11 variants)
• Inborn genetic diseases (10 variants)
• Irido-corneo-trabecular dysgenesis;Aniridia 1 (8 variants)
• not specified (5 variants)
• Aniridia 1;Irido-corneo-trabecular dysgenesis (5 variants)
• Coloboma of optic nerve (4 variants)
• ELP4-related condition (2 variants)
• Aniridia 2 (2 variants)
• PAX6-related ocular dysgenesis (1 variants)
• Hypertelorism;Nystagmus;Visual impairment (1 variants)
• Autism spectrum disorder (1 variants)
• 8 conditions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELP4 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	1	4
missense			16	4	5	25
nonsense			1			1
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding	5	2	58	26	16	107
Total	5	2	75	34	22

Variants in ELP4

This is a list of pathogenic ClinVar variants found in the ELP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-31509799-A-C		ELP4-related disorder	Likely benign (Apr 10, 2019)
11-31509801-C-T		not specified	Uncertain significance (Nov 13, 2023)
11-31509815-G-A		not specified	Likely benign (Mar 12, 2024)
11-31509847-C-G			Likely benign (Mar 07, 2023)
11-31509866-A-G			Uncertain significance (Feb 09, 2023)
11-31509876-G-T		not specified	Uncertain significance (Jan 04, 2024)
11-31509877-G-T			Uncertain significance (May 05, 2023)
11-31509911-G-T			Uncertain significance (Oct 19, 2022)
11-31509949-G-T		ELP4-related disorder	Likely benign (Apr 29, 2022)
11-31510019-G-A			Benign (Apr 20, 2023)
11-31520069-C-T		ELP4-related disorder	Likely benign (May 22, 2019)
11-31520077-C-G		not specified	Uncertain significance (Oct 17, 2023)
11-31539674-A-G		Global developmental delay;Cognitive impairment;Seizure	Likely pathogenic (-)
11-31539685-TC-T		Autism spectrum disorder	association (-)
11-31539728-A-G		not specified	Likely benign (Dec 13, 2022)
11-31539740-T-C			Benign (Jan 29, 2024)
11-31594824-G-T		not specified	Uncertain significance (Dec 13, 2023)
11-31594876-G-A		not specified	Uncertain significance (Sep 27, 2023)
11-31594882-A-C			Uncertain significance (Dec 14, 2023)
11-31603771-G-A		not specified	Uncertain significance (Dec 14, 2023)
11-31603795-G-A			Uncertain significance (Oct 26, 2023)
11-31603802-A-G			Uncertain significance (Apr 10, 2023)
11-31603826-C-A		ELP4-related disorder	Benign/Likely benign (Jan 01, 2024)
11-31603860-A-T			Benign (Oct 28, 2022)
11-31603882-T-C		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELP4	protein_coding	protein_coding	ENST00000350638	10	274250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-7	0.814	124775	0	22	124797	0.0000881

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.300	242	229	1.06	0.0000114	2715
Missense in Polyphen		91	81.913	1.1109		986
Synonymous	-0.456	89	83.7	1.06	0.00000399	848
Loss of Function	1.46	14	21.3	0.658	9.80e-7	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000198	0.000198
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000585	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.0000585	0.0000556
South Asian	0.0000331	0.0000327
Other	0.000179	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as subunit of the RNA polymerase II elongator complex, which is a histone acetyltransferase component of the RNA polymerase II (Pol II) holoenzyme and is involved in transcriptional elongation. Elongator may play a role in chromatin remodeling and is involved in acetylation of histones H3 and probably H4. {ECO:0000269|PubMed:11714725, ECO:0000269|PubMed:11818576, ECO:0000269|PubMed:16713582}.
• Pathway: Mesodermal Commitment Pathway;Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.588
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.74

Haploinsufficiency Scores

• pHI: 0.120
• hipred: Y
• hipred_score: 0.605
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.330

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elp4

Gene ontology

• Biological process: tRNA wobble uridine modification;regulation of transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;regulation of protein kinase activity
• Cellular component: nucleoplasm;cytoplasm;transcription elongation factor complex;Elongator holoenzyme complex
• Molecular function: RNA polymerase II complex binding;protein binding;phosphorylase kinase regulator activity