MTMR6

Summary

MTMR6 (myotubularin related protein 6, HGNC:7453) is a protein-coding gene on chromosome 13q12.13, encoding Phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR6 (Q9Y217). Lipid phosphatase that specifically dephosphorylates the D-3 position of phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate, generating phosphatidylinositol and phosphatidylinositol 5-phosphate.

Enables phosphatidylinositol-3,5-bisphosphate phosphatase activity and phosphatidylinositol-3-phosphate phosphatase activity. Involved in phosphatidylinositol dephosphorylation. Located in cytoplasm and nuclear envelope.

Source: NCBI Gene 9107 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 93 total
• MANE Select transcript: NM_004685

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7453
Approved symbol	MTMR6
Name	myotubularin related protein 6
Location	13q12.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000139505
Ensembl biotype	protein_coding
OMIM	603561
Entrez	9107

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 9 protein_coding

ENST00000381801, ENST00000482345, ENST00000876354, ENST00000876355, ENST00000876356, ENST00000876357, ENST00000876358, ENST00000956554, ENST00000956555

RefSeq mRNA: 10 — MANE Select: NM_004685 NM_001385230, NM_001385231, NM_001385232, NM_001385233, NM_001385234, NM_001385235, NM_001385236, NM_001385237, NM_001385238, NM_004685

CCDS: CCDS9313

Canonical transcript exons

ENST00000381801 — 14 exons

Exon	Start	End
ENSE00000938474	25251649	25251775
ENSE00001239922	25251853	25251984
ENSE00001596599	25261668	25261802
ENSE00001679999	25254385	25254434
ENSE00001681577	25265819	25265947
ENSE00001690721	25267779	25267941
ENSE00001703916	25253764	25253964
ENSE00001720889	25257196	25257321
ENSE00001730864	25274071	25274187
ENSE00001733809	25257736	25257845
ENSE00001788092	25266129	25266286
ENSE00001801114	25258560	25258692
ENSE00001884180	25246222	25249492
ENSE00001912344	25287224	25287488

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 97.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.2570 / max 442.2705, expressed in 1818 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136466	25.8089	1814
136465	4.6735	1330
136462	1.2073	389
136464	0.4654	217
136463	0.4334	176
136461	0.3703	126
136459	0.2031	54
136460	0.0950	31

Top tissues by expression

294 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	97.30	gold quality
Brodmann (1909) area 23	UBERON:0013554	95.85	gold quality
middle temporal gyrus	UBERON:0002771	93.85	silver quality
visceral pleura	UBERON:0002401	93.75	gold quality
palpebral conjunctiva	UBERON:0001812	93.54	gold quality
frontal pole	UBERON:0002795	92.83	gold quality
renal glomerulus	UBERON:0000074	92.68	gold quality
metanephric glomerulus	UBERON:0004736	92.49	gold quality
pleura	UBERON:0000977	92.31	gold quality
parietal pleura	UBERON:0002400	92.18	gold quality
sperm	CL:0000019	92.05	gold quality
dorsal root ganglion	UBERON:0000044	91.92	gold quality
tibia	UBERON:0000979	91.62	gold quality
hair follicle	UBERON:0002073	91.25	silver quality
male germ cell	CL:0000015	91.05	gold quality
periodontal ligament	UBERON:0008266	90.91	gold quality
Brodmann (1909) area 10	UBERON:0013541	90.88	gold quality
upper leg skin	UBERON:0004262	90.78	gold quality
postcentral gyrus	UBERON:0002581	90.72	gold quality
entorhinal cortex	UBERON:0002728	90.62	gold quality
middle frontal gyrus	UBERON:0002702	90.55	gold quality
bronchial epithelial cell	CL:0002328	90.50	gold quality
orbitofrontal cortex	UBERON:0004167	90.44	silver quality
lower lobe of lung	UBERON:0008949	90.01	gold quality
nephron tubule	UBERON:0001231	89.98	gold quality
superior frontal gyrus	UBERON:0002661	89.95	gold quality
parietal lobe	UBERON:0001872	89.69	gold quality
bone marrow	UBERON:0002371	89.57	gold quality
seminal vesicle	UBERON:0000998	89.49	gold quality
adrenal tissue	UBERON:0018303	89.30	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

211 targeting MTMR6, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-1468-3P	99.96	72.74	3797

Literature-anchored findings (GeneRIF, showing 8)

• investigation of MTM1 and MTMR6 and finding that they use PtdIns(3,5)P2 in addition to PtdIns3P as a substrate in vitro (PMID:12646134)
• Identification of myotubularin as the lipid phosphatase catalytic subunit associated with the 3-phosphatase adapter protein, 3-PAP. (PMID:12847286)
• Data show that KCa3.1, which is critical for Ca2+ influx in reactivated naive T cells and central memory T cells, requires phosphatidylinositol-3 phosphatase for activation and is inhibited by PI(3)P phosphatase myotubularin-related protein 6 (MTMR6). (PMID:16847315)
• MTMR9 greatly enhances the functions of MTMR6 (PMID:19038970)
• results indicate that the cellular localization of MTMR6 is regulated by Rab1B in the early secretory and autophagic pathways (PMID:23188820)
• MTMR6, which dephosphorylates PI(3)P to PI, and its binding partner MTMR9, are required for macropinocytosis. (PMID:24591580)
• rescue experiments using MTMR6 overexpression further verified that MTMR6 was a functional target of miR-506-3p. Our data indicate that miR-506-3p might serve as a tumor suppressor gene and propose a new regulatory mechanism of MTMR6 by miR-506-3p in ovarian cancer . (PMID:31894107)
• Myotubularin-related protein 6 is an ion channel-associated pro-leishmanial phosphatase. (PMID:38330797)

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
danio_rerio	mtmr6	ENSDARG00000016794
mus_musculus	Mtmr6	ENSMUSG00000021987
rattus_norvegicus	Mtmr6	ENSRNOG00000012918
drosophila_melanogaster	mtm	FBGN0025742
drosophila_melanogaster	Sbf	FBGN0025802
drosophila_melanogaster	Mtmr6	FBGN0028497
drosophila_melanogaster	CG14411	FBGN0030582
drosophila_melanogaster	CG3632	FBGN0030735
drosophila_melanogaster	CG5026	FBGN0035945
caenorhabditis_elegans	mtm-1	WBGENE00003475
caenorhabditis_elegans		WBGENE00003476
caenorhabditis_elegans		WBGENE00003477
caenorhabditis_elegans		WBGENE00003478
caenorhabditis_elegans		WBGENE00003479
caenorhabditis_elegans	mtm-10	WBGENE00021683

Paralogs (13): MTMR7 (ENSG00000003987), MTMR11 (ENSG00000014914), MTMR1 (ENSG00000063601), MTMR2 (ENSG00000087053), SBF1 (ENSG00000100241), MTMR3 (ENSG00000100330), MTMR8 (ENSG00000102043), MTMR9 (ENSG00000104643), MTMR4 (ENSG00000108389), SBF2 (ENSG00000133812), MTMR12 (ENSG00000150712), MTMR10 (ENSG00000166912), MTM1 (ENSG00000171100)

Protein

Protein identifiers

Phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR6 — Q9Y217 (reviewed: Q9Y217)

Alternative names: Myotubularin-related protein 6, Phosphatidylinositol-3-phosphate phosphatase

All UniProt accessions (2): Q9Y217, A0A9L9PXJ0

UniProt curated annotations — full annotation on UniProt →

Function. Lipid phosphatase that specifically dephosphorylates the D-3 position of phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate, generating phosphatidylinositol and phosphatidylinositol 5-phosphate. Binds with high affinity to phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) but also to phosphatidylinositol 3-phosphate (PtdIns(3)P), phosphatidylinositol 4-phosphate (PtdIns(4)P), and phosphatidylinositol 5-phosphate (PtdIns(5)P), phosphatidic acid and phosphatidylserine. Negatively regulates ER-Golgi protein transport. Probably in association with MTMR9, plays a role in the late stages of macropinocytosis by dephosphorylating phosphatidylinositol 3-phosphate in membrane ruffles. Acts as a negative regulator of KCNN4/KCa3.1 channel activity in CD4(+) T-cells possibly by decreasing intracellular levels of phosphatidylinositol 3-phosphate. Negatively regulates proliferation of reactivated CD4(+) T-cells. In complex with MTMR9, negatively regulates DNA damage-induced apoptosis. The formation of the MTMR6-MTMR9 complex stabilizes both MTMR6 and MTMR9 protein levels.

Subunit / interactions. Homodimer. Heterodimer (via C-terminus) with MTMR9 (via C-terminus). Interacts with ALKBH4. Interacts with KCNN4. Interacts (via GRAM domain) with RAB1B (in GDP-bound form); the interaction regulates MTMR6 recruitment to the endoplasmic reticulum-Golgi intermediate compartment.

Subcellular location. Cytoplasm. Endoplasmic reticulum-Golgi intermediate compartment. Endoplasmic reticulum. Cell projection. Ruffle membrane. Perinuclear region.

Tissue specificity. Expressed in CD4+ T-cells.

Activity regulation. Allosterically activated by phosphatidylserine and/or phosphatidylinositol 4-phosphate (PtdIns(4)P), and phosphatidylinositol 5-phosphate (PtdIns(5)P). Interaction with MTMR9 increases catalytic activity towards phosphatidylinositol 3,5-bisphosphate.

Domain organisation. The GRAM domain is required for cell membrane localization. The C-terminus domain (aa 502-621) mediates interaction with MTMR9.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class myotubularin subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y217-1	1	yes
Q9Y217-2	2

RefSeq proteins (10): NP_001372159, NP_001372160, NP_001372161, NP_001372162, NP_001372163, NP_001372164, NP_001372165, NP_001372166, NP_001372167, NP_004676* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003595	Tyr_Pase_cat	Domain
IPR010569	Myotubularin-like_Pase_dom	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR016130	Tyr_Pase_AS	Active_site
IPR029021	Prot-tyrosine_phosphatase-like	Homologous_superfamily
IPR030564	Myotubularin	Family
IPR035998	MTMR6_PH-GRAM	Domain
IPR048994	PH-GRAM_MTMR6-9	Domain

Pfam: PF06602, PF21098

Enzyme classification (BRENDA):

• EC 3.1.3.95 — phosphatidylinositol-3,5-bisphosphate 3-phosphatase (BRENDA: 2 organisms, 16 substrates, 1 inhibitors, 0 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 4 shown:

• a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate (RHEA:12316)
• a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3,5-bisphosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + phosphate (RHEA:39019)
• 1,2-dioctanoyl-sn-glycero-3-phospho-(1-D-myo-inositol-3-phosphate) + H2O = 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate (RHEA:42328)
• 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol-3,5-bisphosphate) + H2O = 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + phosphate (RHEA:45632)

UniProt features (91 total): helix 24, binding site 21, strand 19, sequence conflict 7, turn 6, modified residue 5, domain 2, splice variant 2, sequence variant 2, chain 1, region of interest 1, active site 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2YF0	X-RAY DIFFRACTION	2.65

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y217-F1	87.66	0.78

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 336 (phosphocysteine intermediate)

Ligand- & substrate-binding residues (21): 274; 337; 337; 338; 338; 339; 339; 340; 340; 341; 341; 342 …

Post-translational modifications (5): 108, 556, 561, 589, 611

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-1660499	Synthesis of PIPs at the plasma membrane
R-HSA-1430728	Metabolism
R-HSA-1483255	PI Metabolism
R-HSA-1483257	Phospholipid metabolism
R-HSA-556833	Metabolism of lipids

MSigDB gene sets: 220 (showing top): GOBP_LIPID_MODIFICATION, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, GOBP_PHOSPHOLIPID_DEPHOSPHORYLATION, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_VESICLE_MEDIATED_TRANSPORT, GOCC_RUFFLE, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, ATGTTAA_MIR302C, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, FISCHER_G2_M_CELL_CYCLE, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS

GO Biological Process (7): protein dephosphorylation (GO:0006470), phosphatidylinositol biosynthetic process (GO:0006661), endocytosis (GO:0006897), phosphatidylinositol dephosphorylation (GO:0046856), lipid metabolic process (GO:0006629), dephosphorylation (GO:0016311), phosphatidylinositol metabolic process (GO:0046488)

GO Molecular Function (7): phosphatidylinositol-3-phosphate phosphatase activity (GO:0004438), protein serine/threonine phosphatase activity (GO:0004722), protein tyrosine phosphatase activity (GO:0004725), phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629), phosphatidylinositol-3,5-bisphosphate phosphatase activity (GO:0106018), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (10): nuclear envelope (GO:0005635), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), cytosol (GO:0005829), ruffle membrane (GO:0032587), perinuclear region of cytoplasm (GO:0048471), plasma membrane (GO:0005886), membrane (GO:0016020), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
PI Metabolism	1
Phospholipid metabolism	1
Metabolism of lipids	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cytoplasm	4
phosphatidylinositol metabolic process	2
phosphoprotein phosphatase activity	2
endomembrane system	2
intracellular membrane-bounded organelle	2
dephosphorylation	1
protein modification process	1
biosynthetic process	1
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
phospholipid dephosphorylation	1
primary metabolic process	1
phosphate-containing compound metabolic process	1
phosphorus metabolic process	1
phosphatidylinositol monophosphate phosphatase activity	1
phosphatidylinositol-3,5-bisphosphate phosphatase activity	1
phosphatidylinositol bisphosphate phosphatase activity	1
binding	1
catalytic activity	1
nucleus	1
organelle envelope	1
intracellular anatomical structure	1
ruffle	1
cell projection membrane	1
leading edge membrane	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1141 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MTMR6	MTMR9	Q96QG7	905
MTMR6	KCNN4	O15554	751
MTMR6	PHPT1	Q9NRX4	655
MTMR6	MTMR14	Q8NCE2	654
MTMR6	SBF1	O95248	609
MTMR6	RAB1B	Q9H0U4	537
MTMR6	PIK3C3	Q8NEB9	518
MTMR6	NME2	P22392	485
MTMR6	SYNJ2	O15056	465
MTMR6	PIKFYVE	Q9Y2I7	441
MTMR6	PIK3C2B	O00750	435
MTMR6	SYNJ1	O43426	430
MTMR6	ZMYM2	Q9UBW7	427
MTMR6	MAMLD1	Q13495	423
MTMR6	TPTE2	Q6XPS3	404

IntAct

82 interactions, top by confidence:

A	B	Type	Score
ZWINT	NDC80	psi-mi:“MI:0914”(association)	0.940
MTMR6	MTMR9	psi-mi:“MI:0915”(physical association)	0.920
MTMR9	MTMR6	psi-mi:“MI:0915”(physical association)	0.920
MTMR6	MTMR9	psi-mi:“MI:2364”(proximity)	0.920
STK25	STRN	psi-mi:“MI:0914”(association)	0.900
MTMR7	CCNH	psi-mi:“MI:0914”(association)	0.740
CDA	LIN7A	psi-mi:“MI:0914”(association)	0.640
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
TRIM27	MTMR6	psi-mi:“MI:0915”(physical association)	0.560
MTMR6	NMI	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	MTMR6	psi-mi:“MI:0915”(physical association)	0.560
AMOTL2	MTMR6	psi-mi:“MI:0915”(physical association)	0.560
NMI	MTMR6	psi-mi:“MI:0915”(physical association)	0.560
MTMR6	MTUS2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (128): MTMR6 (Two-hybrid), NMI (Two-hybrid), MTUS2 (Two-hybrid), AMOTL2 (Two-hybrid), MTMR9 (Two-hybrid), MTMR6 (Affinity Capture-MS), MTMR6 (Affinity Capture-MS), MTMR6 (Affinity Capture-MS), MTMR6 (Co-fractionation), MTMR9 (Co-fractionation), MTMR6 (Proximity Label-MS), MTMR6 (Proximity Label-MS), MTMR6 (Proximity Label-MS), MTMR6 (Proximity Label-MS), MTMR6 (Two-hybrid)

ESM2 similar proteins: A0A0G2JXT6, A0JMF6, A0JMK5, A2ALK8, A2BGG1, A6QLT4, A7MB43, G5ED68, O13819, O14830, P26045, P33402, P51432, Q09M05, Q13496, Q13613, Q15111, Q3USB7, Q4KWH5, Q4R6N0, Q4U2V3, Q52KU6, Q5EB32, Q5F452, Q5R6F6, Q5R9S3, Q5U581, Q62688, Q6AXQ4, Q6NU08, Q6TEL0, Q6XPS3, Q7TPM9, Q7ZXF1, Q8K394, Q8NCE2, Q8VE11, Q8VEL2, Q96EF0, Q96MI9

Diamond homologs: A0A0G2JXT6, A0JMK5, A2BGG1, A4FU01, A6QLT2, A6QLT4, A7MB43, E9PXF8, F4J3T8, F4JWB3, G5ED68, O13819, P47147, Q13496, Q13613, Q13614, Q13615, Q22712, Q2KJ24, Q3V1L6, Q52KU6, Q54GQ1, Q55E58, Q5EB32, Q5F452, Q5PQT2, Q5R6F6, Q5R9S3, Q5REB9, Q5U581, Q5ZIV1, Q6AXQ4, Q6NTN5, Q6NU08, Q6TEL0, Q7TPM9, Q7ZXF1, Q80TA6, Q8K296, Q8VE11

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 87 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Constitutive Signaling by Aberrant PI3K in Cancer	7	15.3×	6e-05
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling	7	11.7×	3e-04
PIP3 activates AKT signaling	9	10.4×	6e-05

GO biological processes:

GO term	Partners	Fold	FDR
protein autophosphorylation	6	11.8×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

93 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2024 predictions. Top by Δscore:

Variant	Effect	Δscore
13:25249489:TTTT:T	acceptor_gain	1.0000
13:25249493:C:CC	acceptor_gain	1.0000
13:25251851:A:AC	donor_gain	1.0000
13:25251852:C:CC	donor_gain	1.0000
13:25253762:A:AC	donor_gain	1.0000
13:25253763:C:CC	donor_gain	1.0000
13:25253779:T:A	donor_gain	1.0000
13:25257734:A:AC	donor_gain	1.0000
13:25257735:C:CT	donor_gain	1.0000
13:25257841:ATTGA:A	acceptor_gain	1.0000
13:25257842:TTGA:T	acceptor_gain	1.0000
13:25257843:TGA:T	acceptor_gain	1.0000
13:25257844:GA:G	acceptor_gain	1.0000
13:25257844:GAC:G	acceptor_loss	1.0000
13:25257845:AC:A	acceptor_loss	1.0000
13:25257846:C:CC	acceptor_gain	1.0000
13:25258555:TATAC:T	donor_loss	1.0000
13:25258556:ATACC:A	donor_loss	1.0000
13:25258557:TACC:T	donor_loss	1.0000
13:25258558:A:T	donor_loss	1.0000
13:25258562:T:A	donor_gain	1.0000
13:25258688:TTCAG:T	acceptor_gain	1.0000
13:25258689:TCAG:T	acceptor_gain	1.0000
13:25258690:CAG:C	acceptor_gain	1.0000
13:25258690:CAGC:C	acceptor_gain	1.0000
13:25258691:AG:A	acceptor_gain	1.0000
13:25258691:AGC:A	acceptor_loss	1.0000
13:25258692:GCTA:G	acceptor_loss	1.0000
13:25258693:C:CC	acceptor_gain	1.0000
13:25258693:C:CG	acceptor_loss	1.0000

AlphaMissense

4130 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:25254385:C:A	R382M	1.000
13:25257265:C:A	R342S	1.000
13:25257265:C:G	R342S	1.000
13:25257266:C:A	R342M	1.000
13:25257269:T:A	D341V	1.000
13:25257269:T:G	D341A	1.000
13:25257273:A:G	W340R	1.000
13:25257273:A:T	W340R	1.000
13:25257275:C:T	G339D	1.000
13:25257278:T:A	D338V	1.000
13:25257283:A:C	C336W	1.000
13:25257285:A:G	C336R	1.000
13:25257786:A:G	W307R	1.000
13:25257786:A:T	W307R	1.000
13:25258594:A:C	H275Q	1.000
13:25258594:A:T	H275Q	1.000
13:25258596:G:C	H275D	1.000
13:25258600:A:C	N273K	1.000
13:25258600:A:T	N273K	1.000
13:25258615:A:C	F268L	1.000
13:25258615:A:T	F268L	1.000
13:25258617:A:G	F268L	1.000
13:25258658:C:T	G254D	1.000
13:25258659:C:G	G254R	1.000
13:25258679:G:T	A247D	1.000
13:25261674:C:A	R240S	1.000
13:25261674:C:G	R240S	1.000
13:25261675:C:A	R240M	1.000
13:25261675:C:G	R240T	1.000
13:25261681:T:G	D238A	1.000

dbSNP variants (sampled 300 via entrez): RS1000031858 (13:25285213 T>G), RS1000040728 (13:25279505 T>A,C), RS1000053336 (13:25287257 A>G), RS1000343088 (13:25255179 T>C), RS1000430710 (13:25261881 C>A,T), RS1000658523 (13:25275295 G>A), RS1000697624 (13:25250179 G>A), RS1000707379 (13:25249680 G>A,C), RS1000707883 (13:25275028 G>A), RS1000714173 (13:25268193 A>G), RS1000771043 (13:25251938 G>C,T), RS1000802420 (13:25248235 G>A), RS1000979287 (13:25282151 T>C), RS1001065005 (13:25289085 C>A), RS1001075622 (13:25263824 T>G)

Disease associations

OMIM: gene MIM:603561 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST009698_1	Metabolite levels	7.000000e-09
GCST010244_191	Triglyceride levels	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

41 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	7
Tetrachlorodibenzodioxin	affects expression, increases expression	2
Tretinoin	decreases expression, increases expression	2
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	decreases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	decreases expression	1
beta-methylcholine	affects expression	1
tamibarotene	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Bortezomib	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Decitabine	increases expression	1
Vorinostat	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Caffeine	increases phosphorylation	1
Cisplatin	affects cotreatment, decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Gold	decreases expression	1
Ivermectin	decreases expression	1
Naphthoquinones	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SZ32	HAP1 MTMR6 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.