TMEM11

Summary

TMEM11 (transmembrane protein 11, HGNC:16823) is a protein-coding gene on chromosome 17p11.2, encoding Transmembrane protein 11, mitochondrial (P17152). Plays a role in mitochondrial morphogenesis.

Involved in mitochondrion organization. Located in mitochondrial inner membrane.

Source: NCBI Gene 8834 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_003876

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16823
Approved symbol	TMEM11
Name	transmembrane protein 11
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	PMI, PM1
Ensembl gene	ENSG00000178307
Ensembl biotype	protein_coding
OMIM	618817
Entrez	8834

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding_CDS_not_defined, 3 protein_coding

ENST00000317635, ENST00000577419, ENST00000583264, ENST00000583929, ENST00000584432, ENST00000584732, ENST00000873639, ENST00000918692

RefSeq mRNA: 1 — MANE Select: NM_003876 NM_003876

CCDS: CCDS11216

Canonical transcript exons

ENST00000317635 — 2 exons

Exon	Start	End
ENSE00001346524	21214091	21214161
ENSE00002712220	21197954	21198840

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.4389 / max 143.4590, expressed in 1820 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164923	33.9254	1820
164924	0.7590	517
164926	0.6776	382
164925	0.0770	27

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	96.95	gold quality
gastrocnemius	UBERON:0001388	96.84	gold quality
muscle of leg	UBERON:0001383	96.64	gold quality
muscle organ	UBERON:0001630	95.36	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.58	gold quality
mucosa of transverse colon	UBERON:0004991	93.12	gold quality
apex of heart	UBERON:0002098	92.76	gold quality
skeletal muscle tissue	UBERON:0001134	92.60	gold quality
triceps brachii	UBERON:0001509	92.28	gold quality
lower esophagus mucosa	UBERON:0035834	92.12	gold quality
biceps brachii	UBERON:0001507	92.11	gold quality
skin of abdomen	UBERON:0001416	91.90	gold quality
skin of leg	UBERON:0001511	91.79	gold quality
heart left ventricle	UBERON:0002084	91.78	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	91.74	gold quality
quadriceps femoris	UBERON:0001377	91.62	gold quality
vastus lateralis	UBERON:0001379	91.62	gold quality
cardiac ventricle	UBERON:0002082	91.47	gold quality
monocyte	CL:0000576	91.13	gold quality
right atrium auricular region	UBERON:0006631	91.06	gold quality
omental fat pad	UBERON:0010414	90.91	gold quality
peritoneum	UBERON:0002358	90.88	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.88	gold quality
adipose tissue of abdominal region	UBERON:0007808	90.82	gold quality
mononuclear cell	CL:0000842	90.79	gold quality
esophagus mucosa	UBERON:0002469	90.71	gold quality
leukocyte	CL:0000738	90.70	gold quality
zone of skin	UBERON:0000014	90.41	gold quality
transverse colon	UBERON:0001157	90.34	gold quality
esophagus	UBERON:0001043	90.14	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.30
E-MTAB-7303	no	232.49

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ZBTB17

miRNA regulators (miRDB)

28 targeting TMEM11, 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-1193	100.00	65.93	529
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-580-5P	99.28	70.94	1776
HSA-MIR-324-3P	99.26	66.31	1034
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-181A-2-3P	98.91	67.60	1168
HSA-MIR-760	98.81	66.65	1392
HSA-MIR-6769B-5P	98.73	64.91	1092
HSA-MIR-4680-3P	98.64	68.60	2093
HSA-MIR-6818-3P	98.56	68.23	1307
HSA-MIR-6769A-5P	97.99	64.16	851
HSA-MIR-558	97.50	67.16	977
HSA-MIR-5187-3P	97.28	67.10	1037
HSA-MIR-5579-5P	96.32	68.54	730
HSA-MIR-541-3P	96.07	66.11	1271
HSA-MIR-654-5P	96.07	66.18	1280
HSA-MIR-6781-5P	94.61	59.49	155
HSA-MIR-6826-5P	93.80	67.42	514

Literature-anchored findings (GeneRIF, showing 2)

• study demonstrates that the Drosophila PMI gene and its human orthologue TMEM11 encode mitochondrial inner-membrane proteins that regulate mitochondrial morphogenesis (PMID:21274005)
• The outer mitochondrial membrane protein TMEM11 demarcates spatially restricted BNIP3/BNIP3L-mediated mitophagy. (PMID:36795401)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem11	ENSDARG00000070866
mus_musculus	Tmem11	ENSMUSG00000043284
rattus_norvegicus	Tmem11	ENSRNOG00000005377
drosophila_melanogaster	Pmi	FBGN0044419

Protein

Protein identifiers

Transmembrane protein 11, mitochondrial — P17152 (reviewed: P17152)

Alternative names: Protein PM1, Protein PMI

All UniProt accessions (1): P17152

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in mitochondrial morphogenesis.

Subunit / interactions. Associates with the mitochondrial contact site and cristae organizing system (MICOS) complex, composed of at least MICOS10/MIC10, CHCHD3/MIC19, CHCHD6/MIC25, APOOL/MIC27, IMMT/MIC60, APOO/MIC23/MIC26 and QIL1/MIC13. This complex was also known under the names MINOS or MitOS complex. The MICOS complex associates with mitochondrial outer membrane proteins SAMM50, MTX1, MTX2 and DNAJC11, mitochondrial inner membrane protein TMEM11 and with HSPA9. Interacts with IMMT/MIC60.

Subcellular location. Mitochondrion inner membrane.

Similarity. Belongs to the TMEM11 family.

RefSeq proteins (1): NP_003867* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026120	TMEM11	Family

Pfam: PF14972

UniProt features (4 total): transmembrane region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17152-F1	79.14	0.28

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8949613	Cristae formation

MSigDB gene sets: 146 (showing top): YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10, MORF_MSH3, MORF_BRCA1, MORF_ATRX, MORF_ESR1, MORF_PPP5C, GOBP_INNER_MITOCHONDRIAL_MEMBRANE_ORGANIZATION, MORF_FANCG, GOCC_MITOCHONDRIAL_ENVELOPE, HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN, MORF_RAP1A, GOBP_MEMBRANE_ORGANIZATION, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN, MORF_MT4, MORF_PPP2R5B

GO Biological Process (2): mitochondrion organization (GO:0007005), inner mitochondrial membrane organization (GO:0007007)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Mitochondrial biogenesis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle organization	1
mitochondrial membrane organization	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1202 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM11	RRAGA	Q7L523	764
TMEM11	RRAGB	Q5VZM2	706
TMEM11	HRAS	P01112	544
TMEM11	RRAGC	Q9HB90	497
TMEM11	RRAGD	Q9NQL2	497
TMEM11	APOOL	Q6UXV4	486
TMEM11	CCR5	P51681	479
TMEM11	SMIM20	Q8N5G0	479
TMEM11	IMMT	Q16891	475
TMEM11	ARL6IP4	Q66PJ3	474
TMEM11	DNAJC11	Q9NVH1	468
TMEM11	MTX2	O75431	454
TMEM11	NUB1	Q9Y5A7	447
TMEM11	TMEM117	Q9H0C3	436
TMEM11	KDELR1	P24390	431

IntAct

238 interactions, top by confidence:

A	B	Type	Score
BNIP3	BNIP3L	psi-mi:“MI:0914”(association)	0.970
BNIP3	TMEM11	psi-mi:“MI:0915”(physical association)	0.920
TMEM11	BNIP3	psi-mi:“MI:0915”(physical association)	0.920
BNIP3L	TMEM11	psi-mi:“MI:0915”(physical association)	0.840
TMEM11	BNIP3L	psi-mi:“MI:0915”(physical association)	0.840
TMEM11	KASH5	psi-mi:“MI:0915”(physical association)	0.700
KASH5	TMEM11	psi-mi:“MI:0915”(physical association)	0.700
TMEM11	FATE1	psi-mi:“MI:0915”(physical association)	0.670
TMEM11	CREB3L1	psi-mi:“MI:0915”(physical association)	0.670
TNFSF14	TMEM11	psi-mi:“MI:0915”(physical association)	0.670
BCAM	LAMA5	psi-mi:“MI:0914”(association)	0.640
LRRC32	SMPD2	psi-mi:“MI:0914”(association)	0.640
TMEM11	MRM1	psi-mi:“MI:0915”(physical association)	0.560
TMEM11	GJB4	psi-mi:“MI:0915”(physical association)	0.560
TMEM11	RNASEH1	psi-mi:“MI:0915”(physical association)	0.560
TMEM11	MUC1	psi-mi:“MI:0915”(physical association)	0.560
TMEM11	YIPF6	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (136): TMEM11 (Two-hybrid), TMEM11 (Two-hybrid), TMEM11 (Affinity Capture-RNA), TMEM11 (Affinity Capture-MS), TMEM11 (Affinity Capture-MS), TMEM11 (Affinity Capture-MS), TMEM11 (Affinity Capture-MS), TMEM11 (Two-hybrid), TMEM11 (Two-hybrid), TMEM11 (Affinity Capture-Western), FATE1 (Two-hybrid), CREB3L1 (Two-hybrid), TMEM11 (Affinity Capture-MS), TMEM11 (Affinity Capture-MS), TMEM11 (Affinity Capture-MS)

ESM2 similar proteins: A2BD92, A4FV45, A5D7N3, A7S641, B0BN86, D3Z2R5, F1Q930, O76024, O95870, P17152, P97587, Q0IJ20, Q17QW2, Q1JPD2, Q1JPG0, Q2HJ63, Q3B8H3, Q4QQM5, Q5BK13, Q5BLE2, Q5RAS8, Q5RJQ8, Q5SWK7, Q5SYH2, Q5ZLD4, Q66H44, Q6DC66, Q6DF19, Q6GR21, Q6MG55, Q6NRI4, Q6NUQ4, Q6NWH5, Q6ZQE4, Q7L4E1, Q7SZC5, Q7ZW11, Q7ZWF4, Q7ZYA0, Q810L4

Diamond homologs: A2BD92, A5D7N3, B0BN86, P17152, Q3B8H3, Q5ZLD4, Q6NWH5, Q8BK08, Q8IQ56

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

607 predictions. Top by Δscore:

Variant	Effect	Δscore
17:21198844:T:C	acceptor_gain	1.0000
17:21198857:C:CT	acceptor_gain	1.0000
17:21198858:A:T	acceptor_gain	1.0000
17:21198840:CCTTT:C	acceptor_gain	0.9900
17:21198844:T:TC	acceptor_gain	0.9900
17:21198847:A:AC	acceptor_gain	0.9900
17:21214085:TCTCA:T	donor_loss	0.9900
17:21214086:CTCA:C	donor_loss	0.9900
17:21214087:TCA:T	donor_loss	0.9900
17:21214088:CA:C	donor_loss	0.9900
17:21214089:A:AT	donor_loss	0.9900
17:21214090:CCTC:C	donor_loss	0.9900
17:21198836:TCACC:T	acceptor_gain	0.9800
17:21198837:CACC:C	acceptor_gain	0.9800
17:21198837:CACCC:C	acceptor_gain	0.9800
17:21198839:CC:C	acceptor_gain	0.9800
17:21198841:C:CC	acceptor_gain	0.9800
17:21198847:A:C	acceptor_gain	0.9800
17:21208442:T:TA	donor_gain	0.9800
17:21214090:CCT:C	donor_gain	0.9800
17:21214090:CCTCT:C	donor_gain	0.9800
17:21214089:A:AC	donor_gain	0.9700
17:21214090:C:CC	donor_gain	0.9700
17:21198843:T:TC	acceptor_gain	0.9600
17:21203736:C:CA	donor_gain	0.9600
17:21198842:T:C	acceptor_gain	0.9500
17:21208405:T:TA	donor_gain	0.9500
17:21214134:T:TA	donor_gain	0.9500
17:21214340:AGT:A	donor_gain	0.9500
17:21198842:T:TC	acceptor_gain	0.9400

AlphaMissense

1224 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:21198427:A:G	L159P	1.000
17:21198427:A:T	L159Q	1.000
17:21198502:T:C	Y134C	1.000
17:21198503:A:G	Y134H	1.000
17:21198517:T:A	D129V	1.000
17:21198525:C:A	W126C	1.000
17:21198525:C:G	W126C	1.000
17:21198527:A:G	W126R	1.000
17:21198527:A:T	W126R	1.000
17:21198670:C:A	G78V	1.000
17:21198670:C:T	G78D	1.000
17:21198671:C:A	G78C	1.000
17:21198671:C:G	G78R	1.000
17:21198683:A:G	W74R	1.000
17:21198683:A:T	W74R	1.000
17:21198700:C:T	G68D	1.000
17:21198718:A:T	I62N	1.000
17:21198724:A:T	I60N	1.000
17:21198745:A:G	L53P	1.000
17:21198757:A:G	L49P	1.000
17:21198427:A:C	L159R	0.999
17:21198430:A:T	V158E	0.999
17:21198499:T:G	Q135P	0.999
17:21198502:T:G	Y134S	0.999
17:21198503:A:C	Y134D	0.999
17:21198510:G:C	C131W	0.999
17:21198511:C:T	C131Y	0.999
17:21198512:A:G	C131R	0.999
17:21198517:T:C	D129G	0.999
17:21198517:T:G	D129A	0.999

dbSNP variants (sampled 300 via entrez): RS1000091112 (17:21208912 G>A), RS1000155343 (17:21207658 C>A,G,T), RS1000229106 (17:21202992 G>A), RS1000239197 (17:21203226 A>T), RS1000351856 (17:21210927 T>A), RS1000588714 (17:21209247 G>A), RS1000594335 (17:21204704 T>C), RS1000863410 (17:21200631 C>G,T), RS1001148476 (17:21199259 G>A), RS1001172428 (17:21214948 C>A,T), RS1001581934 (17:21211326 C>T), RS1001638608 (17:21199076 C>A), RS1001701636 (17:21205968 G>A,C), RS1001862959 (17:21205422 G>C), RS1001929448 (17:21203704 A>G)

Disease associations

OMIM: gene MIM:618817 | 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
GCST005951_14	Body mass index	5.000000e-10
GCST009391_1409	Metabolite levels	7.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0005132	5-HIAA measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, affects cotreatment, increases methylation	2
Tobacco Smoke Pollution	increases expression	2
FR900359	increases phosphorylation	1
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
sodium arsenite	affects binding, increases reaction	1
perfluorooctanoic acid	increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
corosolic acid	decreases expression	1
bisphenol AF	increases expression	1
Decitabine	affects methylation	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Atrazine	decreases expression	1
Ivermectin	decreases expression	1
Smoke	decreases expression	1
Valproic Acid	decreases expression	1
Vitamin E	increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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