METTL17

protein-coding

methyltransferase like 17, the group of 7BS orphan methyltransferases

Gene summary

Enables 4 iron, 4 sulfur cluster binding activity. Involved in mitochondrial small ribosomal subunit assembly. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

METT11D1

MANE transcript

NM_022734.3

Inheritance

—

ClinVar variants

U:71B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr14:20,989,973-20,997,035

External References & Databases

Ensembl (ENSG00000165792)

Transcript & Mutation Effects

hg38 • Region Span ~7.1 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 METTL17 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022734.3. 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 clinvar		2
missense			65 clinvar	4 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	71	5	0	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022734.3	RefSeq	NP_073571.1	14	MANE Select
ENST00000339374.11	Ensembl	ENSP00000343041.6	14	MANE Select
NM_001029991.2	RefSeq	NP_001025162.1	13	Standard
ENST00000382985.8	Ensembl	ENSP00000372445.4	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

translation
methylation

Molecular Function

protein binding
methyltransferase activity

Cellular Component

nucleus
nucleoplasm
mitochondrion
ribosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382985
Coding exons: 13
Length: 7261
Individuals with no LoFs: 125603
Homozygous LoFs: 0
Heterozygous LoFs: 145
Defined: 125748
p: 0.000577

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.523	255	280	0.912	0.0000152	3053
Missense (PolyPhen)		60	90.147	0.66558		1006
Synonymous	-0.756	113	103	1.09	0.00000533	975
Loss of Function	1.31	20	27.4	0.729	0.00000130	310

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.0027	0.0028	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00071	0.00071	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00033	0.00033	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a component of the mitochondrial small ribosomal subunit. {ECO:0000250}.;

Recessive Scores

pRec: 0.0764

Intolerance Scores

RVIS EVS: 0.05
RVIS percentile EVS: 57.48

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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