MTMR11

Summary

MTMR11 (myotubularin related protein 11, HGNC:24307) is a protein-coding gene on chromosome 1q21.2, encoding Myotubularin-related protein 11 (A4FU01).

Predicted to enable phosphatidylinositol-3-phosphate phosphatase activity. Predicted to be involved in phosphatidylinositol dephosphorylation. Located in cytoplasm.

Source: NCBI Gene 10903 — RefSeq curated summary.

At a glance

• GWAS associations: 42
• Clinical variants (ClinVar): 113 total — 1 pathogenic
• MANE Select transcript: NM_001145862

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24307
Approved symbol	MTMR11
Name	myotubularin related protein 11
Location	1q21.2
Locus type	gene with protein product
Status	Approved
Aliases	CRA
Ensembl gene	ENSG00000014914
Ensembl biotype	protein_coding
Entrez	10903

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 7 retained_intron, 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000369140, ENST00000439741, ENST00000466496, ENST00000479272, ENST00000482025, ENST00000482343, ENST00000490310, ENST00000492824, ENST00000493562, ENST00000495054, ENST00000853977, ENST00000853978, ENST00000947774

RefSeq mRNA: 2 — MANE Select: NM_001145862 NM_001145862, NM_181873

CCDS: CCDS72901, CCDS72902

Canonical transcript exons

ENST00000439741 — 17 exons

Exon	Start	End
ENSE00001071744	149933855	149933942
ENSE00001334613	149931260	149931426
ENSE00001334623	149933610	149933698
ENSE00003459070	149936154	149936229
ENSE00003465699	149933406	149933530
ENSE00003480110	149934191	149934326
ENSE00003493045	149935299	149935359
ENSE00003548663	149932264	149932330
ENSE00003558563	149936582	149936879
ENSE00003594784	149935584	149935705
ENSE00003596073	149930365	149930547
ENSE00003622663	149934448	149934526
ENSE00003635487	149934986	149935128
ENSE00003639058	149929623	149929916
ENSE00003650254	149930792	149930965
ENSE00003660863	149928651	149929317
ENSE00003672290	149931944	149932014

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 97.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2408 / max 230.3128, expressed in 1431 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14279	4.4546	1185
14275	4.1539	625
14274	1.0217	97
14277	0.3737	59
14276	0.1948	86
14278	0.0421	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	97.85	gold quality
rectum	UBERON:0001052	97.82	gold quality
ileal mucosa	UBERON:0000331	97.57	gold quality
transverse colon	UBERON:0001157	96.86	gold quality
jejunal mucosa	UBERON:0000399	96.69	gold quality
descending thoracic aorta	UBERON:0002345	95.57	gold quality
duodenum	UBERON:0002114	95.27	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.24	gold quality
colonic mucosa	UBERON:0000317	94.93	gold quality
thoracic aorta	UBERON:0001515	94.84	gold quality
ascending aorta	UBERON:0001496	94.83	gold quality
right ovary	UBERON:0002118	94.56	gold quality
small intestine	UBERON:0002108	94.53	gold quality
right adrenal gland	UBERON:0001233	94.28	gold quality
left ovary	UBERON:0002119	94.27	gold quality
mucosa of sigmoid colon	UBERON:0004993	94.19	gold quality
aorta	UBERON:0000947	94.16	gold quality
monocyte	CL:0000576	94.14	gold quality
intestine	UBERON:0000160	93.85	gold quality
right coronary artery	UBERON:0001625	93.81	gold quality
left adrenal gland cortex	UBERON:0035825	93.77	gold quality
popliteal artery	UBERON:0002250	93.76	gold quality
mononuclear cell	CL:0000842	93.75	gold quality
tibial artery	UBERON:0007610	93.75	gold quality
left adrenal gland	UBERON:0001234	93.69	gold quality
right adrenal gland cortex	UBERON:0035827	93.68	gold quality
large intestine	UBERON:0000059	93.67	gold quality
colon	UBERON:0001155	93.63	gold quality
gall bladder	UBERON:0002110	93.52	gold quality
leukocyte	CL:0000738	93.40	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.05
E-MTAB-9801	yes	6.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting MTMR11, 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-4425	100.00	67.59	1049
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-3913-5P	99.78	67.26	968
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-3199	99.17	65.19	696
HSA-MIR-8052	99.17	65.01	719
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-9500	98.62	66.54	1845
HSA-MIR-890	97.47	68.67	982
HSA-MIR-15A-3P	97.47	65.08	527
HSA-MIR-1225-3P	97.29	64.60	876
HSA-MIR-6892-5P	97.27	68.60	847
HSA-MIR-1233-3P	96.81	65.44	573
HSA-MIR-4529-5P	96.74	65.77	569
HSA-MIR-6769A-3P	94.91	61.36	412

Literature-anchored findings (GeneRIF, showing 1)

• Genome wide association study shows evidence of association between mammographic density and SNPs in high linkage disequilibrium with rs11205277, rs11205303 in gene MTMR11 and rs67807996 in gene OTUD7B. (PMID:25353672)

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
danio_rerio	mtmr11	ENSDARG00000069755
mus_musculus	Mtmr11	ENSMUSG00000045934
rattus_norvegicus	Mtmr11	ENSRNOG00000021176
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), MTMR1 (ENSG00000063601), MTMR2 (ENSG00000087053), SBF1 (ENSG00000100241), MTMR3 (ENSG00000100330), MTMR8 (ENSG00000102043), MTMR9 (ENSG00000104643), MTMR4 (ENSG00000108389), SBF2 (ENSG00000133812), MTMR6 (ENSG00000139505), MTMR12 (ENSG00000150712), MTMR10 (ENSG00000166912), MTM1 (ENSG00000171100)

Protein

Protein identifiers

Myotubularin-related protein 11 — A4FU01 (reviewed: A4FU01)

Alternative names: Cisplatin resistance-associated protein, Inactive phosphatidylinositol 3-phosphatase 11

All UniProt accessions (1): A4FU01

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in bone marrow, spleen and thymus.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

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

Isoforms (6)

UniProt ID	Names	Canonical?
A4FU01-1	1	yes
A4FU01-2	2, hCRA alpha
A4FU01-3	3
A4FU01-4	4
A4FU01-5	5, hCRA beta
A4FU01-6	6

RefSeq proteins (2): NP_001139334, NP_870988 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010569	Myotubularin-like_Pase_dom	Domain
IPR022587	MTMR12-like_C	Domain
IPR029021	Prot-tyrosine_phosphatase-like	Homologous_superfamily
IPR030564	Myotubularin	Family

Pfam: PF06602, PF12578

UniProt features (18 total): splice variant 10, sequence conflict 3, sequence variant 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4FU01-F1	74.50	0.36

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 162 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, RACCACAR_AML_Q6, BROWNE_HCMV_INFECTION_48HR_DN, HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN, CAIRO_HEPATOBLASTOMA_CLASSES_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, BRN2_01, OCT1_03, BROWNE_HCMV_INFECTION_24HR_DN, AML1_01, HNF1_01, TGGAAA_NFAT_Q4_01, chr1q21, OSF2_Q6, GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): cytoplasm (GO:0005737), membrane (GO:0016020), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
intracellular anatomical structure	1
extracellular vesicle	1

Protein interactions and networks

STRING

547 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MTMR11	MTMR12	Q9C0I1	479
MTMR11	MTMR10	Q9NXD2	449
MTMR11	OR10H2	O60403	447
MTMR11	GRPEL1	Q9HAV7	436
MTMR11	NT5DC1	Q5TFE4	422
MTMR11	TMEM184B	Q9Y519	419
MTMR11	TPST1	O60507	402
MTMR11	ZNF182	P17025	385
MTMR11	TMEM205	Q6UW68	367
MTMR11	TENT5A	Q96IP4	355
MTMR11	ZNF567	Q8N184	336
MTMR11	STYXL1	Q9Y6J8	330
MTMR11	IPMK	Q8NFU5	326
MTMR11	RBM38	Q9H0Z9	317
MTMR11	PHTF2	Q8N3S3	310

IntAct

5 interactions, top by confidence:

A	B	Type	Score
MTMR11	EPHA3	psi-mi:“MI:0915”(physical association)	0.370
MTMR11	SMAD9	psi-mi:“MI:0915”(physical association)	0.370
	MTMR11	psi-mi:“MI:0914”(association)	0.350
MTMR11	HSPA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (23): AIFM1 (Affinity Capture-MS), CAD (Affinity Capture-MS), COX4I1 (Affinity Capture-MS), DNAJA1 (Affinity Capture-MS), DNAJA2 (Affinity Capture-MS), DNAJA3 (Affinity Capture-MS), FKBP8 (Affinity Capture-MS), IRS4 (Affinity Capture-MS), CCAR2 (Affinity Capture-MS), LONP1 (Affinity Capture-MS), MTM1 (Affinity Capture-MS), MTMR2 (Affinity Capture-MS), TIMM50 (Affinity Capture-MS), TUBB6 (Affinity Capture-MS), MTMR11 (Two-hybrid)

ESM2 similar proteins: A0JMF6, A2BGG1, A4FU01, B1WC10, E7FAW3, E9PUQ8, E9PXF8, F4JWB3, O00750, O15327, O70167, O70173, O95248, O95876, P0CE43, P97874, Q2I0E5, Q2I6J0, Q32NR9, Q3V1L6, Q4R4D7, Q5PQT2, Q5R991, Q5RA60, Q5U581, Q5ZLG9, Q60760, Q60949, Q68DX3, Q6NTN5, Q6NU08, Q6P1Y8, Q6PJI9, Q6ZPE2, Q6ZS30, Q7TPM9, Q7ZXF1, Q80U56, Q86WG5, Q8C0M0

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	91
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
393786	GRCh37/hg19 1q21.2(chr1:149895368-150130518)x1	Pathogenic

SpliceAI

2504 predictions. Top by Δscore:

Variant	Effect	Δscore
1:149933705:A:C	acceptor_gain	1.0000
1:149934187:TCA:T	donor_loss	1.0000
1:149934188:CA:C	donor_loss	1.0000
1:149934190:CC:C	donor_loss	1.0000
1:149934322:CTGGC:C	acceptor_gain	1.0000
1:149934323:TGGC:T	acceptor_gain	1.0000
1:149934324:GGC:G	acceptor_gain	1.0000
1:149934325:GC:G	acceptor_gain	1.0000
1:149934326:CC:C	acceptor_gain	1.0000
1:149934327:C:CC	acceptor_gain	1.0000
1:149934333:C:CT	acceptor_gain	1.0000
1:149934334:A:T	acceptor_gain	1.0000
1:149934338:G:C	acceptor_gain	1.0000
1:149934338:G:GC	acceptor_gain	1.0000
1:149934345:A:C	acceptor_gain	1.0000
1:149935292:AACTT:A	donor_loss	1.0000
1:149935293:ACTT:A	donor_loss	1.0000
1:149935294:CTTAC:C	donor_loss	1.0000
1:149935295:TTACC:T	donor_loss	1.0000
1:149935297:A:AT	donor_loss	1.0000
1:149935298:C:CA	donor_loss	1.0000
1:149935298:CCAG:C	donor_gain	1.0000
1:149935701:CTCCC:C	acceptor_gain	1.0000
1:149935703:CCC:C	acceptor_gain	1.0000
1:149935704:CC:C	acceptor_gain	1.0000
1:149935704:CCC:C	acceptor_gain	1.0000
1:149935705:CC:C	acceptor_gain	1.0000
1:149935705:CCTA:C	acceptor_loss	1.0000
1:149935706:C:CA	acceptor_loss	1.0000
1:149935706:C:CC	acceptor_gain	1.0000

AlphaMissense

4578 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:149931319:A:G	W411R	0.997
1:149931319:A:T	W411R	0.997
1:149934223:G:C	S217R	0.996
1:149934223:G:T	S217R	0.996
1:149934225:T:G	S217R	0.996
1:149932280:A:G	W346R	0.995
1:149932280:A:T	W346R	0.995
1:149934234:A:G	W214R	0.993
1:149934234:A:T	W214R	0.993
1:149933664:A:G	L269P	0.992
1:149929661:A:G	W635R	0.990
1:149929661:A:T	W635R	0.990
1:149930466:A:G	W516R	0.990
1:149930466:A:T	W516R	0.990
1:149930925:A:G	L444P	0.990
1:149932006:A:G	L354P	0.990
1:149931317:C:A	W411C	0.989
1:149931317:C:G	W411C	0.989
1:149931998:C:G	A357P	0.989
1:149933489:A:T	V301D	0.988
1:149934214:G:C	N220K	0.988
1:149934214:G:T	N220K	0.988
1:149933661:A:G	L270P	0.987
1:149933922:A:T	V235D	0.987
1:149931955:A:T	V371E	0.986
1:149932278:C:A	W346C	0.985
1:149932278:C:G	W346C	0.985
1:149929659:C:A	W635C	0.983
1:149929659:C:G	W635C	0.983
1:149930464:C:A	W516C	0.983

dbSNP variants (sampled 300 via entrez): RS1000623324 (1:149929590 T>C,G), RS1000743503 (1:149929236 T>C), RS1001907372 (1:149928480 C>A,G), RS1002256578 (1:149928737 G>A,C,T), RS1002669144 (1:149933394 G>A,C), RS1003511623 (1:149938199 G>A), RS1004186117 (1:149938615 A>G), RS1004244360 (1:149936312 A>C,G), RS1004699713 (1:149936074 G>A,C,T), RS1005298326 (1:149934689 G>A), RS1005376519 (1:149928703 A>G), RS1006470926 (1:149933917 T>C), RS1008995288 (1:149937670 C>T), RS1010460260 (1:149934085 G>C), RS1010882180 (1:149938654 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

42 associations (top):

Study	Trait	p-value
GCST000175_50	Height	1.000000e-10
GCST001956_6	Height	4.000000e-23
GCST004067_12	Hip circumference adjusted for BMI	6.000000e-25
GCST004067_125	Hip circumference adjusted for BMI	2.000000e-13
GCST004067_207	Hip circumference adjusted for BMI	2.000000e-16
GCST004562_10	Waist circumference adjusted for body mass index	4.000000e-09
GCST004562_192	Waist circumference adjusted for body mass index	8.000000e-09
GCST004562_211	Waist circumference adjusted for body mass index	2.000000e-07
GCST004562_256	Waist circumference adjusted for body mass index	8.000000e-14
GCST004562_69	Waist circumference adjusted for body mass index	3.000000e-08
GCST004562_79	Waist circumference adjusted for body mass index	6.000000e-16
GCST004563_146	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	5.000000e-08
GCST004563_157	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	1.000000e-07
GCST004563_217	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	8.000000e-12
GCST004563_40	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	2.000000e-06
GCST004563_56	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	6.000000e-14
GCST004563_76	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	7.000000e-07
GCST004564_20	Waist circumference adjusted for BMI in active individuals	3.000000e-06
GCST004564_21	Waist circumference adjusted for BMI in active individuals	2.000000e-07
GCST004564_22	Waist circumference adjusted for BMI in active individuals	1.000000e-10
GCST004564_23	Waist circumference adjusted for BMI in active individuals	4.000000e-06
GCST004564_24	Waist circumference adjusted for BMI in active individuals	3.000000e-06
GCST004564_25	Waist circumference adjusted for BMI in active individuals	4.000000e-11
GCST007294_101	Body fat distribution (trunk fat ratio)	2.000000e-87
GCST007294_115	Body fat distribution (trunk fat ratio)	3.000000e-22
GCST007294_154	Body fat distribution (trunk fat ratio)	4.000000e-99
GCST007295_122	Body fat distribution (leg fat ratio)	1.000000e-76
GCST007295_14	Body fat distribution (leg fat ratio)	4.000000e-23
GCST007295_98	Body fat distribution (leg fat ratio)	5.000000e-92
GCST008156_32	Hip circumference adjusted for BMI	6.000000e-07

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference
EFO:0007789	BMI-adjusted waist circumference
EFO:0008002	physical activity measurement
EFO:0004341	body fat distribution
EFO:0009819	comparative body size at age 10, self-reported

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	2
Cisplatin	affects expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Cyclosporine	increases expression	2
FR900359	increases phosphorylation	1
bufotalin	decreases expression	1
daidzein	affects cotreatment, decreases expression	1
methyleugenol	increases expression	1
propionaldehyde	decreases expression	1
sodium arsenate	decreases expression, increases abundance	1
daidzin	affects cotreatment, decreases expression	1
beta-lapachone	increases expression	1
sulforaphane	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
genistin	affects cotreatment, decreases expression	1
pentanal	decreases expression	1
glycitein	affects cotreatment, decreases expression	1
entinostat	increases expression	1
glycitin	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
NSC 689534	increases expression, affects binding	1
bisphenol AF	increases expression	1
Rosiglitazone	decreases expression	1
Decitabine	affects expression	1
Arsenic Trioxide	decreases expression	1
Acetaminophen	decreases expression	1

Clinical trials (associated diseases)

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