HEMK1

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

Basic information

Region (hg38): 3:50569152-50596168

Links

ENSG00000114735 ∙ NCBI:51409 ∙ OMIM:618609 ∙ HGNC:24923 ∙ Uniprot:Q9Y5R4 ∙ 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 HEMK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEMK1 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			32	3		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	33	3	0

Variants in HEMK1

This is a list of pathogenic ClinVar variants found in the HEMK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50571121-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-50571139-T-C		not specified	Uncertain significance (Sep 30, 2024)
3-50571144-G-C		not specified	Uncertain significance (Feb 13, 2025)
3-50571154-G-C		not specified	Uncertain significance (Jul 15, 2024)
3-50571169-G-A		not specified	Likely benign (Nov 17, 2022)
3-50571177-G-C		not specified	Uncertain significance (Mar 26, 2025)
3-50571210-G-T		not specified	Uncertain significance (Nov 07, 2024)
3-50571214-G-A		not specified	Uncertain significance (Jan 22, 2024)
3-50571268-G-A		not specified	Uncertain significance (Mar 04, 2025)
3-50571306-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-50571330-A-G		not specified	Uncertain significance (Mar 19, 2024)
3-50571726-C-T		not specified	Uncertain significance (Feb 05, 2024)
3-50571743-C-G		not specified	Uncertain significance (Feb 16, 2023)
3-50571753-C-T		not specified	Uncertain significance (Apr 03, 2025)
3-50571788-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-50571789-G-A		not specified	Uncertain significance (Jan 19, 2024)
3-50572194-C-T		not specified	Uncertain significance (Jul 16, 2021)
3-50577058-G-A		not specified	Uncertain significance (Jun 05, 2024)
3-50577071-T-G		not specified	Uncertain significance (Nov 10, 2024)
3-50577092-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-50577118-C-T		not specified	Uncertain significance (Oct 09, 2024)
3-50577154-A-G		not specified	Uncertain significance (Jun 17, 2024)
3-50577513-G-A		not specified	Likely benign (Jun 06, 2025)
3-50577533-C-T		not specified	Uncertain significance (Mar 28, 2024)
3-50577545-A-C		not specified	Uncertain significance (Dec 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEMK1	protein_coding	protein_coding	ENST00000232854	10	15784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.39e-8	0.782	125652	0	96	125748	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.528	179	200	0.895	0.0000117	2182
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00102
Ashkenazi Jewish	0.00437	0.00437
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.000652	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0444
• hipred: N
• hipred_score: 0.237
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hemk1

Gene ontology

• Biological process: DNA methylation;protein methylation
• Cellular component: mitochondrion
• Molecular function: DNA binding;protein binding;N-methyltransferase activity;protein methyltransferase activity