ELP5

elongator acetyltransferase complex subunit 5, the group of Elongator acetyltransferase complex

Basic information

Region (hg38): 17:7251416-7259940

Previous symbols: [ "C17orf81" ]

Links

ENSG00000170291 ∙ NCBI:23587 ∙ OMIM:615019 ∙ HGNC:30617 ∙ Uniprot:Q8TE02 ∙ 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 ELP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELP5 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						0
missense			21	1	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2	1		3
Total	0	0	23	2	2

Variants in ELP5

This is a list of pathogenic ClinVar variants found in the ELP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7252510-C-T		not specified	Likely benign (Mar 22, 2023)
17-7252534-C-T		not specified	Uncertain significance (Jan 18, 2022)
17-7252540-G-T		not specified	Uncertain significance (Jul 15, 2021)
17-7252567-T-C		not specified	Uncertain significance (Apr 11, 2023)
17-7252593-C-G		not specified	Uncertain significance (Jul 14, 2022)
17-7252820-T-C		not specified	Uncertain significance (Sep 14, 2021)
17-7252940-G-T		not specified	Uncertain significance (Sep 14, 2023)
17-7252967-C-T		not specified	Uncertain significance (Jun 16, 2023)
17-7252997-C-T		not specified	Uncertain significance (Mar 14, 2023)
17-7253002-A-C			Benign (Feb 20, 2018)
17-7254644-C-A		not specified	Uncertain significance (Nov 18, 2022)
17-7254645-C-T		not specified	Uncertain significance (May 23, 2023)
17-7254647-G-A		not specified	Uncertain significance (Mar 25, 2024)
17-7254654-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-7254657-T-G		not specified	Uncertain significance (Nov 07, 2023)
17-7254686-A-G		not specified	Uncertain significance (Oct 04, 2022)
17-7254740-C-T		not specified	Uncertain significance (Oct 20, 2023)
17-7254791-G-A		not specified	Uncertain significance (Jun 10, 2022)
17-7256959-A-G		not specified	Uncertain significance (Jan 17, 2024)
17-7257019-G-A		not specified	Likely benign (Aug 02, 2021)
17-7257024-C-T		not specified	Uncertain significance (Jun 22, 2023)
17-7258601-C-T		not specified	Uncertain significance (Dec 14, 2021)
17-7258637-G-A			Benign (Feb 25, 2018)
17-7258639-C-G		not specified	Uncertain significance (Jun 24, 2022)
17-7258827-T-C			Benign (Feb 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELP5	protein_coding	protein_coding	ENST00000396628	8	8525

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.08e-13	0.00883	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0311	179	178	1.01	0.00000893	2040
Missense in Polyphen		65	65.021	0.99968		809
Synonymous	-0.789	81	72.5	1.12	0.00000375	646
Loss of Function	-0.592	18	15.5	1.16	7.33e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00210	0.00210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.000761	0.000707
South Asian	0.000230	0.000229
Other	0.000326	0.000326

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. Involved in cell migration (By similarity). May be involved in TP53-mediated transcriptional regulation. {ECO:0000250, ECO:0000269|PubMed:16850183}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.0882

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.246
• hipred: N
• hipred_score: 0.123
• ghis: 0.494

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elp5

Gene ontology

• Biological process: tRNA wobble uridine modification;positive regulation of cell migration
• Cellular component: nucleus;cytoplasm;cytosol;Elongator holoenzyme complex
• Molecular function: protein binding