MTMR10

protein-coding

myotubularin related protein 10, the group of Myotubularins

Gene summary

Located in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017762.3

Inheritance

—

ClinVar variants

U:118B:4

Top phenotype

Karyomegalic interstitial nephritis

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr15:30,938,941-30,991,628

External References & Databases

Ensembl (ENSG00000166912)

Transcript & Mutation Effects

hg38 • Region Span ~52.7 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 MTMR10 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 1

Karyomegalic interstitial nephritisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017762.3. 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			4 clinvar	1 clinvar		5
missense			109 clinvar	3 clinvar		112
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	118	4	0	122

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017762.3	RefSeq	NP_060232.2	16	MANE Select
ENST00000435680.6	Ensembl	ENSP00000402537.1	16	MANE Select
ENST00000563714.5	Ensembl	ENSP00000457390.1	13	Standard
ENST00000564787.1	Ensembl	ENSP00000455903.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
TCR
Metabolism
Synthesis of PIPs at the early endosome membrane
PI Metabolism

Cellular Component

cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000435680
Coding exons: 16
Length: 52667
Individuals with no LoFs: 124609
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 124641
p: 0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	318	388	0.819	0.0000201	5071
Missense (PolyPhen)		89	145	0.61379		1976
Synonymous	-0.852	165	152	1.09	0.00000884	1434
Loss of Function	3.17	18	39.5	0.455	0.00000201	507

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00013	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00024	0.00022	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable pseudophosphatase. Contains a Glu residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase (Potential). {ECO:0000305}.;

Intolerance Scores

LoFtool: 0.0593
RVIS EVS: 0.38
RVIS percentile EVS: 75.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0457

Gene Damage Prediction

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