EEF1AKMT1

Chr 13

EEF1A lysine methyltransferase 1

Also known as: ESP13, N6AMT2, eEF1A-KMT

NCBI Gene: 221143 ENSG00000150456 UniProt: Q8WVE0

The protein is a methyltransferase that specifically trimethylates elongation factor EEF1A at lysine-79, which is involved in protein synthesis. Mutations cause autosomal recessive intellectual disability with distinctive facial features and developmental delays. This gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely incompatible with normal development.

ResearchSummary from RefSeq, UniProt

Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.57

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.57LOEUF

pLI 0.000

Z-score 0.25

OE 0.91 (0.55–1.57)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.25Z-score

OE missense 0.94 (0.80–1.09)

112 obs / 119.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.91 (0.55–1.57)

0≤0.351.4

Missense OE?0.94 (0.80–1.09)

0≤0.61.4

Synonymous OE?1.16

0≤1.21.6

LoF obs/exp: 9 / 9.8Missense obs/exp: 112 / 119.8Syn Z: -0.86

Background carrier burden — how many people carry a rare variant somewhere in EEF1AKMT1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 240

256 rare PASS variants

Rare truncating (LoF)

1 in 3,600

46 rare PASS variants

Rare synonymous (reference)

1 in 550

117 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for EEF1AKMT1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 290	1 in 3,800
South Asian	~43k	1 in 130	1 in 2,400
Remaining (unassigned)	~30k	1 in 250	≈ 1 in 15,000
European (Finnish)	~27k	1 in 610	1 in 3,300
Admixed American	~22k	1 in 320	≈ 1 in 4,500
African / African American	~21k	1 in 370	1 in 3,000
East Asian	~20k	1 in 310	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 210	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 210	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓