MTMR9

myotubularin related protein 9, the group of Myotubularins

Basic information

Region (hg38): 8:11284815-11328146

Previous symbols: [ "C8orf9", "MTMR8" ]

Links

ENSG00000104643 ∙ NCBI:66036 ∙ OMIM:606260 ∙ HGNC:14596 ∙ Uniprot:Q96QG7 ∙ 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 MTMR9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR9 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					2	2
missense			42	3	2	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	3	4

Variants in MTMR9

This is a list of pathogenic ClinVar variants found in the MTMR9 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-11284947-C-A		not specified	Uncertain significance (Jun 07, 2023)
8-11285001-T-C		not specified	Uncertain significance (Feb 06, 2024)
8-11285057-G-A		not specified	Uncertain significance (Mar 06, 2023)
8-11295246-A-T		not specified	Uncertain significance (May 08, 2023)
8-11295251-G-T		not specified	Uncertain significance (May 13, 2024)
8-11295294-T-A		not specified	Uncertain significance (Jul 29, 2023)
8-11300030-C-T		not specified	Uncertain significance (Mar 06, 2023)
8-11300035-C-G		not specified	Uncertain significance (Apr 06, 2023)
8-11300038-G-C		not specified	Uncertain significance (Dec 06, 2022)
8-11300059-C-G		not specified	Uncertain significance (Jan 26, 2022)
8-11300072-G-A		not specified	Uncertain significance (Dec 12, 2023)
8-11300087-T-G		not specified	Uncertain significance (Feb 28, 2023)
8-11300096-A-G		not specified	Uncertain significance (Aug 08, 2022)
8-11300105-A-G		not specified	Uncertain significance (Jan 09, 2024)
8-11300108-C-G			Benign (Jun 26, 2018)
8-11300138-A-C		not specified	Uncertain significance (Dec 15, 2022)
8-11304848-A-C		not specified	Uncertain significance (Aug 26, 2022)
8-11304863-A-C		not specified	Uncertain significance (Jun 27, 2022)
8-11304883-G-A		not specified	Uncertain significance (Dec 19, 2022)
8-11304889-C-G			Likely benign (Dec 01, 2022)
8-11304968-G-A		not specified	Uncertain significance (Jan 04, 2024)
8-11304987-A-C			Benign (Mar 10, 2022)
8-11306250-G-C		not specified	Uncertain significance (Nov 14, 2023)
8-11306308-G-A		not specified	Uncertain significance (Aug 15, 2023)
8-11306311-C-G		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR9	protein_coding	protein_coding	ENST00000221086	10	43722

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00126	0.999	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.33	418	304	1.38	0.0000157	3605
Missense in Polyphen		80	86.318	0.9268		990
Synonymous	-4.01	167	113	1.48	0.00000586	1035
Loss of Function	3.46	11	32.2	0.341	0.00000184	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.000111	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable pseudophosphatase. Contains a Gly 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;Metabolism;Inositol phosphate metabolism;Synthesis of PIPs at the plasma membrane;Synthesis of PIPs at the late endosome membrane;PI Metabolism;Phospholipid metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.0637
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.94

Haploinsufficiency Scores

• pHI: 0.0965
• hipred: N
• hipred_score: 0.492
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.882

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtmr9

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;negative regulation of autophagy;positive regulation of phosphatase activity;dephosphorylation;protein stabilization;regulation of phosphatidylinositol dephosphorylation
• Cellular component: cytoplasm;cytosol;protein-containing complex
• Molecular function: phosphatidylinositol-3-phosphatase activity;protein binding;protein phosphatase binding;enzyme regulator activity;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity