ELP6

elongator acetyltransferase complex subunit 6, the group of Elongator acetyltransferase complex

Basic information

Region (hg38): 3:47495640-47513712

Previous symbols: [ "TMEM103", "C3orf75" ]

Links

ENSG00000163832 ∙ NCBI:54859 ∙ OMIM:615020 ∙ HGNC:25976 ∙ Uniprot:Q0PNE2 ∙ 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 ELP6 gene.

• not_specified (37 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001031703.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	31	6		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	31	6	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELP6	protein_coding	protein_coding	ENST00000296149	7	18122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000498	0.889	124738	0	75	124813	0.000300

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.405	142	156	0.909	0.00000891	1748
Missense in Polyphen		39	52.176	0.74746		667
Synonymous	1.21	55	67.7	0.813	0.00000427	524
Loss of Function	1.42	7	12.4	0.565	5.25e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000339	0.000338
Ashkenazi Jewish	0.00	0.00
East Asian	0.000614	0.000612
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000362	0.000362
Middle Eastern	0.000614	0.000612
South Asian	0.000359	0.000360
Other	0.00	0.00

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.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.0588
• hipred: N
• hipred_score: 0.248
• ghis: 0.541

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: Elp6
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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