EEF2KMT

protein-coding

eukaryotic elongation factor 2 lysine methyltransferase, the group of 7BS protein lysine methyltransferases

Gene summary

Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation. Located in cytoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM86A

MANE transcript

NM_201400.4

Inheritance

—

ClinVar variants

U:85B:8

Top phenotype

ALG1-congenital disorder of glycosylation

gnomAD constraint

pLI —, LoF o/e 1.27

Max pathogenic AF

—

Genomic locus

chr16:5,084,284-5,097,795

External References & Databases

Ensembl (ENSG00000118894)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 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 EEF2KMT variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 2

ALG1-congenital disorder of glycosylationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_201400.4. 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						0
missense			81 clinvar	8 clinvar		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	85	8	0	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_201400.4	RefSeq	NP_958802.1	8	MANE Select
ENST00000427587.9	Ensembl	ENSP00000398502.3	8	MANE Select
NM_001289029.2	RefSeq	NP_001275958.1	6	Standard
NM_201598.4	RefSeq	NP_963892.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
Protein methylation

Biological Process

protein methylation
peptidyl-lysine trimethylation

Molecular Function

protein binding
protein-lysine N-methyltransferase activity

Cellular Component

cytoplasm
cytosol
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000427587
Coding exons: 8
Length: 13505
Individuals with no LoFs: 125439
Homozygous LoFs: 1
Heterozygous LoFs: 151
Defined: 125591
p: 0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.92	274	198	1.38	0.0000133	2078
Missense (PolyPhen)		34	29.588	1.1491		408
Synonymous	-2.40	117	88.3	1.33	0.00000628	678
Loss of Function	-0.981	20	15.8	1.27	7.62e-7	180

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00077	0.00074	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.0010	0.0010	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00055	0.00055	rare
South Asian	0.0013	0.0012	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the trimethylation of eukaryotic elongation factor 2 (EEF2) on 'Lys-525'. {ECO:0000269|PubMed:25231979}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

RVIS EVS: 1.62
RVIS percentile EVS: 96.01

Essentials

Essential (gene trap): N