ELP3

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

Basic information

Region (hg38): 8:28089673-28191156

Links

ENSG00000134014

∙ NCBI:55140 ∙ OMIM:612722 ∙ HGNC:20696 ∙ Uniprot:Q9H9T3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELP3 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					2 clinvar	2
missense			28 clinvar			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	0	2

Variants in ELP3

This is a list of pathogenic ClinVar variants found in the ELP3 region.

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

Position	Phenotype	Significance	ClinVar
8-28093219-G-A	not specified	Uncertain significance (Dec 27, 2022)	3088515
8-28099847-G-A	not specified	Uncertain significance (Dec 03, 2024)	3508112
8-28099858-C-A		Benign (Jul 06, 2018)	776307
8-28099890-T-C	not specified	Uncertain significance (Mar 07, 2024)	3088512
8-28099941-C-T	not specified	Uncertain significance (Dec 07, 2024)	3508110
8-28106734-T-A	not specified	Uncertain significance (Jun 24, 2022)	2296249
8-28106762-G-A	not specified	Uncertain significance (Nov 02, 2023)	3088513
8-28107913-A-T	not specified	Likely benign (May 06, 2024)	3275245
8-28107932-G-A	not specified	Uncertain significance (Jul 26, 2022)	2303599
8-28110384-A-C	not specified	Uncertain significance (Nov 20, 2023)	3088514
8-28113155-A-G	not specified	Uncertain significance (Nov 15, 2021)	2261407
8-28129564-G-A	not specified	Uncertain significance (Sep 30, 2024)	3508109
8-28129568-GA-G		not provided (-)	440939
8-28129573-G-A	not specified	Uncertain significance (Jan 10, 2023)	2458262
8-28129618-T-C	not specified	Uncertain significance (Jan 23, 2024)	3088516
8-28132342-G-A	not specified	Uncertain significance (Apr 22, 2024)	3275246
8-28132351-A-G	not specified	Uncertain significance (Jun 02, 2023)	2513474
8-28132391-T-G		not provided (-)	440940
8-28137712-C-G	not specified	Uncertain significance (May 13, 2024)	3275248
8-28137740-C-T	not specified	Uncertain significance (Dec 28, 2022)	2340215
8-28137876-T-C	not specified	Uncertain significance (Dec 14, 2022)	2272259
8-28155961-G-A	not specified	Uncertain significance (Jun 23, 2023)	2600184
8-28156024-G-A	not specified	Uncertain significance (Nov 15, 2024)	3508113
8-28158572-G-A	not specified	Uncertain significance (Aug 02, 2021)	2208737
8-28160243-G-C	not specified	Uncertain significance (Jun 02, 2023)	2540338

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELP3	protein_coding	protein_coding	ENST00000256398	15	101484

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.01e-14	0.429	125661	0	87	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	228	320	0.712	0.0000175	3553
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000495	0.000489
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000405	0.000404
Middle Eastern	0.000495	0.000489
South Asian	0.000400	0.000392
Other	0.000490	0.000489

dbNSFP

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}.;
Pathway: Ethanol effects on histone modifications;Chromatin modifying enzymes;TCR;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.159

Intolerance Scores

loftool: 0.420
rvis_EVS: -1.07
rvis_percentile_EVS: 7.37

Haploinsufficiency Scores

pHI: 0.172
hipred: Y
hipred_score: 0.578
ghis: 0.643

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Elp3
Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; digestive/alimentary phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name: elp3
Affected structure: motor neuron
Phenotype tag: abnormal
Phenotype quality: decreased length

Gene ontology

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;histone acetylation;positive regulation of cell migration;regulation of protein kinase activity
Cellular component: nucleus;nucleolus;cytoplasm;transcription elongation factor complex;Elongator holoenzyme complex
Molecular function: RNA polymerase II complex binding;histone acetyltransferase activity;protein binding;phosphorylase kinase regulator activity;acetyltransferase activity;metal ion binding;iron-sulfur cluster binding