MTMR10

myotubularin related protein 10, the group of Myotubularins

Basic information

Region (hg38): 15:30938941-30991628

Links

ENSG00000166912 ∙ NCBI:54893 ∙ ∙ HGNC:25999 ∙ Uniprot:Q9NXD2 ∙ 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 MTMR10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR10 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
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	2	0

Variants in MTMR10

This is a list of pathogenic ClinVar variants found in the MTMR10 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-30941618-G-A		not specified	Uncertain significance (Jul 20, 2022)
15-30941625-C-T		not specified	Uncertain significance (Sep 26, 2024)
15-30941634-G-A		not specified	Uncertain significance (Aug 31, 2022)
15-30941699-C-G		not specified	Uncertain significance (Dec 13, 2022)
15-30941706-G-A		not specified	Uncertain significance (Mar 04, 2024)
15-30941714-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-30941722-C-G		not specified	Uncertain significance (Jan 18, 2023)
15-30941733-C-T		not specified	Uncertain significance (Jun 16, 2024)
15-30941735-T-C		not specified	Uncertain significance (Aug 20, 2024)
15-30941749-C-A			Likely benign (May 01, 2022)
15-30941797-C-G		not specified	Uncertain significance (Feb 10, 2022)
15-30941819-AAGT-A		Karyomegalic interstitial nephritis	Uncertain significance (Nov 09, 2018)
15-30941862-G-A		not specified	Uncertain significance (Dec 04, 2024)
15-30941871-T-C		not specified	Uncertain significance (Dec 16, 2023)
15-30941883-G-C		not specified	Uncertain significance (Jan 23, 2023)
15-30941928-C-T		not specified	Uncertain significance (Aug 01, 2024)
15-30941935-C-G		not specified	Uncertain significance (Oct 20, 2024)
15-30941938-G-C		not specified	Uncertain significance (Aug 19, 2023)
15-30941997-G-C		not specified	Uncertain significance (May 30, 2024)
15-30942041-G-C		not specified	Uncertain significance (Sep 26, 2023)
15-30942923-C-G		not specified	Likely benign (Nov 21, 2024)
15-30942961-T-C		not specified	Uncertain significance (Jul 27, 2024)
15-30942976-G-A		not specified	Uncertain significance (Sep 01, 2021)
15-30943012-C-G		not specified	Uncertain significance (May 23, 2024)
15-30943059-C-T		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR10	protein_coding	protein_coding	ENST00000435680	16	52667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-7	1.00	124609	0	32	124641	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	318	388	0.819	0.0000201	5071
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000287	0.000278
Ashkenazi Jewish	0.000104	0.0000994
East Asian	0.000238	0.000223
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000109	0.000106
Middle Eastern	0.000238	0.000223
South Asian	0.000202	0.000196
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Metabolism of lipids;TCR;Metabolism;Synthesis of PIPs at the early endosome membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.0593
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.0435
• hipred: Y
• hipred_score: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0457

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtmr10

Gene ontology

• Cellular component: cytoplasm;cytosol