TMEM52B

Summary

TMEM52B (transmembrane protein 52B, HGNC:26438) is a protein-coding gene on chromosome 12p13.2, encoding Transmembrane protein 52B (Q4KMG9).

Located in extracellular exosome.

Source: NCBI Gene 120939 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_001384896

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26438
Approved symbol	TMEM52B
Name	transmembrane protein 52B
Location	12p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31166
Ensembl gene	ENSG00000165685
Ensembl biotype	protein_coding
Entrez	120939

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000298530, ENST00000334148, ENST00000381923, ENST00000543484, ENST00000545924, ENST00000546153, ENST00000859442, ENST00000859443, ENST00000859444, ENST00000965685, ENST00000965686, ENST00000965687, ENST00000965688

RefSeq mRNA: 7 — MANE Select: NM_001384896 NM_001079815, NM_001384894, NM_001384895, NM_001384896, NM_001384897, NM_001384898, NM_153022

CCDS: CCDS66314, CCDS8619

Canonical transcript exons

ENST00000543484 — 5 exons

Exon	Start	End
ENSE00001095454	10185330	10185368
ENSE00001095458	10186420	10186589
ENSE00001490295	10182550	10182593
ENSE00002293090	10179032	10179628
ENSE00003917506	10189896	10191804

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 98.80.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2361 / max 169.4156, expressed in 235 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
124142	0.3592	87
124137	0.3498	53
124141	0.1332	74
124135	0.1153	39
124139	0.1139	40
124134	0.0955	63
124136	0.0593	13
124138	0.0099	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	98.80	gold quality
adult mammalian kidney	UBERON:0000082	96.62	gold quality
kidney	UBERON:0002113	92.61	gold quality
renal medulla	UBERON:0000362	84.58	gold quality
adult organism	UBERON:0007023	82.64	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.89	gold quality
bone marrow cell	CL:0002092	79.88	gold quality
cortex of kidney	UBERON:0001225	79.48	gold quality
metanephros cortex	UBERON:0010533	78.80	gold quality
metanephros	UBERON:0000081	76.87	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.97	gold quality
placenta	UBERON:0001987	70.19	gold quality
spinal cord	UBERON:0002240	70.02	gold quality
bone marrow	UBERON:0002371	69.79	gold quality
upper lobe of left lung	UBERON:0008952	68.08	gold quality
upper lobe of lung	UBERON:0008948	67.55	gold quality
right lung	UBERON:0002167	67.28	gold quality
buccal mucosa cell	CL:0002336	66.52	silver quality
prefrontal cortex	UBERON:0000451	65.85	gold quality
caudate nucleus	UBERON:0001873	64.18	gold quality
vermiform appendix	UBERON:0001154	63.52	gold quality
putamen	UBERON:0001874	63.50	gold quality
amniotic fluid	UBERON:0000173	63.12	gold quality
monocyte	CL:0000576	62.73	gold quality
leukocyte	CL:0000738	61.55	gold quality
lung	UBERON:0002048	59.91	gold quality
substantia nigra	UBERON:0002038	59.36	gold quality
caecum	UBERON:0001153	58.44	gold quality
frontal cortex	UBERON:0001870	58.32	gold quality
anterior cingulate cortex	UBERON:0009835	58.23	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-CURD-135	yes	3749.53
E-CURD-119	yes	65.03
E-MTAB-6819	yes	48.80
E-HCAD-10	yes	27.71
E-ANND-3	yes	12.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

80 targeting TMEM52B, 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-4673	100.00	66.64	1490
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311

Literature-anchored findings (GeneRIF, showing 2)

• Study showed that C12orf59 was broadly expressed in normal human tissues with high expression levels in kidney while its expression is beyond detectable in a panel of cancer cell lines. (PMID:26758419)
• TMEM52B suppression promotes cancer cell survival and invasion through modulating E-cadherin stability and EGFR activity. (PMID:33641663)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tmem52b	ENSMUSG00000030160
rattus_norvegicus	Tmem52b	ENSRNOG00000058653

Protein

Protein identifiers

Transmembrane protein 52B — Q4KMG9 (reviewed: Q4KMG9)

All UniProt accessions (2): Q4KMG9, F5H230

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q4KMG9-1	1	yes
Q4KMG9-2	2

RefSeq proteins (7): NP_001073283, NP_001371823, NP_001371824, NP_001371825, NP_001371826, NP_001371827, NP_694567 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038942	TMEM52	Family

Pfam: PF14979

UniProt features (6 total): signal peptide 1, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q4KMG9-F1	60.59	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, RORA1_01, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, CHEN_METABOLIC_SYNDROM_NETWORK, STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN, GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_2H_DN, PAX3_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR96_5P, MIR1827, MIR4446_5P, MIR3124_3P, MIR12119

GO Biological Process (0):

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

GO Cellular Component (2): membrane (GO:0016020), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1
extracellular vesicle	1

Protein interactions and networks

STRING

414 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM52B	AQP6	Q13520	478
TMEM52B	KCNJ1	P48048	470
TMEM52B	PLA2G4E	Q3MJ16	469
TMEM52B	SLC12A3	P55017	464
TMEM52B	UMOD	P07911	456
TMEM52B	MIOX	Q9UGB7	433
TMEM52B	CAPN3	P20807	431
TMEM52B	RPL3L	Q92901	402
TMEM52B	TMEM38A	Q9H6F2	396
TMEM52B	ANKRD23	Q86SG2	387
TMEM52B	BSND	Q8WZ55	378
TMEM52B	TMEM213	A2RRL7	376
TMEM52B	RBP5	P82980	370
TMEM52B	CLEC18B	Q6UXF7	370
TMEM52B	MYL11	Q96A32	366

IntAct

207 interactions, top by confidence:

A	B	Type	Score
GAST	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
APOL3	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	TTMP	psi-mi:“MI:0915”(physical association)	0.560
TUSC5	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	SERP1	psi-mi:“MI:0915”(physical association)	0.560
GPR37L1	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	ZDHHC15	psi-mi:“MI:0915”(physical association)	0.560
IGFBP5	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	SLC30A8	psi-mi:“MI:0915”(physical association)	0.560
TMEM267	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	TMEM60	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	NINJ2	psi-mi:“MI:0915”(physical association)	0.560
SMIM1	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
VAMP5	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	TMEM128	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	JAGN1	psi-mi:“MI:0915”(physical association)	0.560
BET1	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	MS4A13	psi-mi:“MI:0915”(physical association)	0.560
TF	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	CSGALNACT2	psi-mi:“MI:0915”(physical association)	0.560
MAL	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
NSG1	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
CNIH1	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
ITGAM	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	ORMDL1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (133): THAP11 (Affinity Capture-MS), NEDD4L (Affinity Capture-MS), NEDD4 (Affinity Capture-MS), RHBDF2 (Affinity Capture-MS), ATP2B4 (Affinity Capture-MS), ANKRD13D (Affinity Capture-MS), FCN1 (Affinity Capture-MS), FLT4 (Affinity Capture-MS), RAB6A (Affinity Capture-MS), ZDHHC9 (Affinity Capture-MS), CORO2A (Affinity Capture-MS), LRBA (Affinity Capture-MS), TAB1 (Affinity Capture-MS), TMEM205 (Affinity Capture-MS), WDR44 (Affinity Capture-MS)

ESM2 similar proteins: A2AR95, A4IHY6, B7ZWI3, D3ZF92, O15165, O43278, O75509, O88204, P98153, P98154, Q0VBF2, Q1L8G6, Q29RU0, Q4KMG9, Q566M8, Q5DTZ6, Q5HZW5, Q5R662, Q5R8E0, Q5RD34, Q5RF74, Q5VUB5, Q61003, Q68FU0, Q6AXS2, Q6NRX0, Q6UWW9, Q6ZPS6, Q6ZUJ8, Q7TQH7, Q86YD5, Q8BGN6, Q8BLD6, Q8BUJ9, Q8R182, Q8TEB7, Q8WUU8, Q91ZV2, Q91ZV3, Q96PD2

Diamond homologs: Q0VBF2, Q4KMG9, Q8NDY8, Q9D702

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

646 predictions. Top by Δscore:

Variant	Effect	Δscore
12:10172007:G:C	donor_gain	1.0000
12:10189893:CA:C	acceptor_loss	1.0000
12:10189894:A:AG	acceptor_gain	1.0000
12:10189894:A:AT	acceptor_loss	1.0000
12:10189895:G:GA	acceptor_gain	1.0000
12:10189895:GC:G	acceptor_gain	1.0000
12:10189895:GCT:G	acceptor_gain	1.0000
12:10189895:GCTCT:G	acceptor_gain	1.0000
12:10170861:C:A	donor_gain	0.9900
12:10171996:TAGTA:T	donor_loss	0.9900
12:10171998:GTACC:G	donor_loss	0.9900
12:10171999:TACC:T	donor_loss	0.9900
12:10172000:ACCTT:A	donor_loss	0.9900
12:10172026:T:TA	donor_gain	0.9900
12:10179123:G:GT	donor_gain	0.9900
12:10185328:A:AG	acceptor_gain	0.9900
12:10185329:G:GG	acceptor_gain	0.9900
12:10186456:T:TA	acceptor_gain	0.9900
12:10189892:A:AG	acceptor_gain	0.9900
12:10189893:C:G	acceptor_gain	0.9900
12:10189895:GCTC:G	acceptor_gain	0.9900
12:10179625:CCTGG:C	donor_loss	0.9800
12:10179627:TGG:T	donor_loss	0.9800
12:10179628:GGTG:G	donor_loss	0.9800
12:10179629:GT:G	donor_loss	0.9800
12:10179630:TGAGT:T	donor_loss	0.9800
12:10179631:GA:G	donor_loss	0.9800
12:10185329:GTT:G	acceptor_gain	0.9800
12:10186454:T:TA	acceptor_gain	0.9800
12:10186484:T:A	acceptor_gain	0.9800

AlphaMissense

558 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:10186436:G:C	G52R	0.950
12:10186454:T:C	C58R	0.942
12:10186437:G:A	G52D	0.935
12:10186458:G:A	G59D	0.913
12:10185358:T:A	W43R	0.911
12:10185358:T:C	W43R	0.911
12:10186449:T:G	L56R	0.904
12:10186472:T:C	C64R	0.901
12:10185367:T:A	W46R	0.894
12:10185367:T:C	W46R	0.894
12:10186457:G:C	G59R	0.886
12:10186449:T:A	L56H	0.868
12:10186548:T:A	I89N	0.865
12:10186545:T:A	V88D	0.859
12:10185348:G:C	W39C	0.853
12:10185348:G:T	W39C	0.853
12:10185360:G:C	W43C	0.838
12:10185360:G:T	W43C	0.838
12:10186548:T:G	I89S	0.827
12:10186443:T:G	L54R	0.826
12:10186446:T:G	L55R	0.821
12:10186542:C:T	T87I	0.797
12:10186440:C:A	A53E	0.791
12:10185365:T:A	I45K	0.776
12:10186428:T:A	V49E	0.770
12:10186446:T:A	L55H	0.762
12:10186452:T:G	L57R	0.752
12:10186425:T:G	L48R	0.743
12:10186461:T:G	L60R	0.738
12:10185361:T:G	Y44D	0.737

dbSNP variants (sampled 300 via entrez): RS1000114217 (12:10171346 G>A), RS1000351781 (12:10180653 A>C), RS1000392931 (12:10168850 A>C), RS1000690907 (12:10180600 A>G), RS1000750203 (12:10185498 T>A), RS1000789153 (12:10168564 G>C), RS1000922865 (12:10186132 G>T), RS1000992075 (12:10192183 A>G,T), RS1001091279 (12:10180178 T>C), RS1001170734 (12:10171934 C>A,T), RS1001320835 (12:10177817 T>A), RS1001383332 (12:10177570 T>C), RS1001427988 (12:10177762 G>C), RS1001433899 (12:10183243 C>A), RS1001531596 (12:10182601 T>C,G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
aristolochic acid I	increases expression	1
bisphenol A	decreases methylation	1
perfluorooctanoic acid	decreases expression	1
nickel sulfate	increases expression	1
perfluorobutyric acid	decreases expression	1
dicyclohexyl phthalate	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression	1
abrine	increases expression	1
prothioconazole	increases expression	1
Zoledronic Acid	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Valproic Acid	increases expression	1
Vanadates	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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