ELP3

protein-coding

elongator acetyltransferase complex subunit 3, the group of Lysine acetyltransferases|Elongator acetyltransferase complex |GCN5 related N-acetyltransferases|Radical S-adenosylmethionine domain containing

Gene summary

Enables acetyltransferase activity. Involved in regulation of transcription by RNA polymerase II and tRNA wobble uridine modification. Located in cytosol and nucleolus. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018091.6

Inheritance

—

ClinVar variants

U:71B:3

Top phenotype

Amyotrophic lateral sclerosis

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr8:28,089,673-28,191,156

External References & Databases

Ensembl (ENSG00000134014)

Transcript & Mutation Effects

hg38 • Region Span ~101.5 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 ELP3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 6

Amyotrophic lateral sclerosisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018091.6. 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			1 clinvar	1 clinvar	2 clinvar	4
missense			61 clinvar			61
nonsense						0
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	71	1	2	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018091.6	RefSeq	NP_060561.3	15	MANE Select
ENST00000256398.13	Ensembl	ENSP00000256398.8	15	MANE Select
NM_001284220.2	RefSeq	NP_001271149.1	13	Standard
NM_001284222.2	RefSeq	NP_001271151.1	14	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
elp3	Danio rerio	Structure: motor neuron Quality: decreased length abnormal

Gene / Model

Organism

Observed Phenotype

elp3

Danio rerio

Structure: motor neuron

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ethanol effects on histone modifications
Chromatin modifying enzymes
TCR
HATs acetylate histones
Chromatin organization

Biological Process

neuron migration
tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation
regulation of transcription by RNA polymerase II
transcription elongation from RNA polymerase II promoter
central nervous system development

Molecular Function

RNA polymerase II complex binding
histone acetyltransferase activity
protein binding
phosphorylase kinase regulator activity
acetyltransferase activity

Cellular Component

nucleus
nucleolus
cytoplasm
transcription elongation factor complex
Elongator holoenzyme complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000256398
Coding exons: 15
Length: 101484
Individuals with no LoFs: 125661
Homozygous LoFs: 0
Heterozygous LoFs: 87
Defined: 125748
p: 0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.83	228	320	0.712	0.0000175	3553
Missense (PolyPhen)		46	97.475	0.47192		1082
Synonymous	0.353	109	114	0.958	0.00000624	1060
Loss of Function	1.44	26	35.2	0.738	0.00000213	388

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00050	0.00049	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.00040	0.00039	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalytic histone acetyltransferase subunit of the RNA polymerase II elongator complex, which is a 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. Involved in acetylation of alpha-tubulin (PubMed:19185337). May also have a methyltransferase activity. Involved in cell migration. Involved in neurogenesis. Regulates the migration and branching of projection neurons in the developing cerebral cortex, through a process depending on alpha- tubulin acetylation. {ECO:0000250|UniProtKB:Q9CZX0, ECO:0000269|PubMed:11714725, ECO:0000269|PubMed:11818576, ECO:0000269|PubMed:15902492, ECO:0000269|PubMed:16713582, ECO:0000269|PubMed:19185337}.;

Recessive Scores

pRec: 0.159

Intolerance Scores

LoFtool: 0.420
RVIS EVS: -1.07
RVIS percentile EVS: 7.37

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.638

Gene Damage Prediction

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