METTL13

protein-coding

methyltransferase 13, eEF1A lysine and N-terminal methyltransferase, the group of 7BS protein lysine methyltransferases

Gene summary

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

Previous symbols:

KIAA0859
DFNM1
EEF1AKNMT

MANE transcript

NM_015935.5

Inheritance

ClinVar variants

U:122B:16

Top phenotype

Deafness, nonsyndromic, modifier 1

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr1:171,781,660-171,814,023

External References & Databases

Ensembl (ENSG00000010165)

Transcript & Mutation Effects

hg38 • Region Span ~32.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Deafness, nonsyndromic, modifier 1AD

Manifestation: Audiologic/Otolaryngologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Comments: Heterozygous variants have a protective effect (related to nonsyndromic deafness) for individuals with homozygous pathogenic variants in GAB1

Refs: 29408807

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to METTL13 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 119

METTL13-related disorderTotal: 13

Deafness, autosomal recessive 26, modifier ofTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015935.5. 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			2 clinvar	8 clinvar	4 clinvar	14
missense			118 clinvar	2 clinvar	2 clinvar	122
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	122	10	6	138

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015935.5	RefSeq	NP_057019.3	8	MANE Select
ENST00000361735.4	Ensembl	ENSP00000354920.3	8	MANE Select
NM_001007239.2	RefSeq	NP_001007240.1	8	Standard
NM_014955.3	RefSeq	NP_055770.1	7	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361735
Coding exons: 8
Length: 32376
Individuals with no LoFs: 125680
Homozygous LoFs: 1
Heterozygous LoFs: 67
Defined: 125748
p: 0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	350	409	0.855	0.0000239	4579
Missense (PolyPhen)		88	123.15	0.71456		1350
Synonymous	-0.332	169	164	1.03	0.00000902	1398
Loss of Function	2.04	19	31.3	0.606	0.00000192	315

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00031	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00039	0.00038	rare
South Asian	0.00015	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Intolerance Scores

RVIS EVS: -0.66
RVIS percentile EVS: 15.95

Essentials

Essential (gene trap): N