HEMK1

protein-coding

HemK methyltransferase family member 1, the group of 7BS protein methyltransferases

Gene summary

Enables peptide chain release factor N(5)-glutamine methyltransferase activity. Predicted to be involved in translational termination. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016173.5

Inheritance

—

ClinVar variants

U:47B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr3:50,569,152-50,596,168

External References & Databases

Ensembl (ENSG00000114735)

Transcript & Mutation Effects

hg38 • Region Span ~27.0 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 HEMK1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016173.5. 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			1 clinvar			1
missense			45 clinvar	5 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	47	5	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 111 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016173.5	RefSeq	NP_057257.1	10	MANE Select
ENST00000232854.9	Ensembl	ENSP00000232854.4	10	MANE Select
NM_001317851.2	RefSeq	NP_001304780.1	10	Standard
NM_001377420.1	RefSeq	NP_001364349.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA methylation
protein methylation

Molecular Function

DNA binding
protein binding
N-methyltransferase activity
protein methyltransferase activity

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000232854
Coding exons: 10
Length: 15784
Individuals with no LoFs: 125652
Homozygous LoFs: 0
Heterozygous LoFs: 96
Defined: 125748
p: 0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.528	179	200	0.895	0.0000117	2182
Missense (PolyPhen)		38	48.17	0.78887		579
Synonymous	1.00	66	77.2	0.855	0.00000407	691
Loss of Function	1.44	15	22.4	0.671	0.00000119	213

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.0044	0.0044	notable
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000065	0.000065	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: N5-glutamine methyltransferase responsible for the methylation of the GGQ triplet of the mitochondrial translation release factor MTRF1L. {ECO:0000269|PubMed:18541145}.;

Recessive Scores

pRec: 0.174

Intolerance Scores

RVIS EVS: 0.04
RVIS percentile EVS: 57.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0959

Gene Damage Prediction

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