EEF1AKMT3

EEF1A lysine methyltransferase 3, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 12:57771492-57782541

Previous symbols: [ "FAM119B", "METTL21B" ]

Links

ENSG00000123427 ∙ NCBI:25895 ∙ OMIM:615258 ∙ HGNC:24936 ∙ Uniprot:Q96AZ1 ∙ 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 EEF1AKMT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1AKMT3 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in EEF1AKMT3

This is a list of pathogenic ClinVar variants found in the EEF1AKMT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57771977-C-T		not specified	Uncertain significance (Aug 17, 2022)
12-57772047-C-T		not specified	Uncertain significance (Aug 15, 2023)
12-57772050-C-G		not specified	Uncertain significance (Nov 27, 2023)
12-57772071-T-G		not specified	Uncertain significance (Jun 18, 2024)
12-57772830-T-C		not specified	Uncertain significance (Feb 06, 2024)
12-57772848-A-T		not specified	Uncertain significance (Mar 04, 2024)
12-57773027-T-A		not specified	Uncertain significance (Dec 03, 2021)
12-57773047-C-G		not specified	Uncertain significance (Apr 13, 2022)
12-57773057-A-T		not specified	Uncertain significance (Aug 08, 2023)
12-57773077-A-T		not specified	Uncertain significance (Nov 29, 2021)
12-57773083-C-G		not specified	Uncertain significance (Apr 25, 2022)
12-57780255-G-A		not specified	Uncertain significance (Jun 17, 2024)
12-57780255-G-T		not specified	Uncertain significance (Jun 11, 2021)
12-57780260-G-C		not specified	Uncertain significance (May 30, 2024)
12-57780296-C-A		not specified	Uncertain significance (Dec 27, 2022)
12-57780311-G-A		not specified	Uncertain significance (Oct 25, 2023)
12-57780354-C-G		not specified	Uncertain significance (Dec 28, 2022)
12-57780484-T-A		not specified	Uncertain significance (May 30, 2024)
12-57780492-T-C			Likely benign (Dec 01, 2022)
12-57780495-A-G		not specified	Uncertain significance (Dec 08, 2023)
12-57780568-A-T		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF1AKMT3	protein_coding	protein_coding	ENST00000300209	3	11050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000311	0.596	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.831	103	130	0.795	0.00000606	1463
Missense in Polyphen		49	54.481	0.8994		609
Synonymous	1.50	45	59.7	0.753	0.00000281	480
Loss of Function	0.596	6	7.79	0.770	3.37e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000218	0.000217
South Asian	0.0000654	0.0000653
Other	0.000819	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine methyltransferase that selectively methylates EEF1A1 and EEF1A2 at 'Lys-165' in an aminoacyl-tRNA and GTP-dependent manner. EEF1A1 methylation by EEF1AKMT3 is dynamic as well as inducible by stress conditions, such as ER-stress, and plays a regulatory role on mRNA translation. {ECO:0000269|PubMed:28108655}.

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.468
• ghis: 0.412

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Eef1akmt3

Gene ontology

• Biological process: peptidyl-lysine methylation
• Cellular component: cytoplasm;centrosome;protein-containing complex
• Molecular function: protein binding;methyltransferase activity;protein-lysine N-methyltransferase activity;heat shock protein binding