HENMT1

HEN methyltransferase 1, the group of 7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): 1:108648289-108661526

Previous symbols: [ "C1orf59" ]

Links

ENSG00000162639 ∙ NCBI:113802 ∙ OMIM:612178 ∙ HGNC:26400 ∙ Uniprot:Q5T8I9 ∙ 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 HENMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HENMT1 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				1	1	2
missense			17	3	2	22
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	4	3

Variants in HENMT1

This is a list of pathogenic ClinVar variants found in the HENMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-108648594-T-G		not specified	Uncertain significance (Apr 24, 2023)
1-108648597-C-T		not specified	Likely benign (Aug 02, 2021)
1-108648598-G-A		not specified	Likely benign (Mar 28, 2024)
1-108648634-G-C		not specified	Uncertain significance (Jan 03, 2022)
1-108648676-T-C			Benign (Aug 02, 2017)
1-108648687-C-T		not specified	Likely benign (Aug 30, 2022)
1-108648727-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-108648771-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-108650246-G-C		not specified	Likely benign (Feb 28, 2023)
1-108650278-C-T			Benign (May 18, 2018)
1-108650300-A-G		not specified	Uncertain significance (Mar 27, 2023)
1-108650330-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-108650337-G-A			Likely benign (Jul 01, 2023)
1-108650351-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-108650378-C-A		not specified	Uncertain significance (Sep 14, 2022)
1-108651066-T-C		not specified	Uncertain significance (Jul 09, 2021)
1-108651152-G-C		Azoospermia	Pathogenic (Dec 20, 2021)
1-108651208-T-A		not specified • Male infertility	Uncertain significance (Feb 27, 2023)
1-108654728-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-108654743-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-108654748-C-A		not specified	Uncertain significance (Mar 23, 2022)
1-108654776-C-G		not specified	Uncertain significance (Feb 14, 2023)
1-108654845-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-108655596-G-A		not specified	Uncertain significance (May 04, 2022)
1-108655623-C-T		Azoospermia	Pathogenic (Dec 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HENMT1	protein_coding	protein_coding	ENST00000370032	7	13237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.82e-10	0.0736	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0585	213	215	0.989	0.0000114	2554
Missense in Polyphen		40	46.078	0.8681		560
Synonymous	0.113	79	80.3	0.984	0.00000410	765
Loss of Function	-0.0435	14	13.8	1.01	6.71e-7	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000262	0.000262
Ashkenazi Jewish	0.00	0.00
East Asian	0.000496	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000496	0.000489
South Asian	0.000199	0.000196
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methyltransferase that adds a 2'-O-methyl group at the 3'-end of piRNAs, a class of 24 to 30 nucleotide RNAs that are generated by a Dicer-independent mechanism and are primarily derived from transposons and other repeated sequence elements. This probably protects the 3'-end of piRNAs from uridylation activity and subsequent degradation. Stabilization of piRNAs is essential for gametogenesis. {ECO:0000250|UniProtKB:Q8CAE2}.
• Pathway: Gene expression (Transcription);PIWI-interacting RNA (piRNA) biogenesis;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.146
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Henmt1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: henmt1
• Affected structure: RNA 3' uridylation
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: RNA methylation;production of siRNA involved in RNA interference;piRNA metabolic process
• Cellular component: nucleus;cytoplasm;P granule
• Molecular function: RNA binding;protein binding;O-methyltransferase activity;RNA methyltransferase activity;metal ion binding