TMEM52

Summary

TMEM52 (transmembrane protein 52, HGNC:27916) is a protein-coding gene on chromosome 1p36.33, encoding Transmembrane protein 52 (Q8NDY8).

Predicted to be located in membrane.

Source: NCBI Gene 339456 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_178545

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27916
Approved symbol	TMEM52
Name	transmembrane protein 52
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000178821
Ensembl biotype	protein_coding
Entrez	339456

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000310991, ENST00000378598, ENST00000378602, ENST00000416272, ENST00000470931, ENST00000602604, ENST00000902364, ENST00000966688

RefSeq mRNA: 1 — MANE Select: NM_178545 NM_178545

CCDS: CCDS35

Canonical transcript exons

ENST00000310991 — 5 exons

Exon	Start	End
ENSE00001239803	1919182	1919279
ENSE00001754010	1917591	1918162
ENSE00003473336	1919045	1919088
ENSE00003634508	1918893	1918934
ENSE00003675447	1918253	1918431

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 98.69.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0622 / max 175.2709, expressed in 549 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9857	1.9954	540
9856	0.0668	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	98.69	gold quality
body of pancreas	UBERON:0001150	98.56	gold quality
gastrocnemius	UBERON:0001388	96.84	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.79	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.21	gold quality
vastus lateralis	UBERON:0001379	95.86	gold quality
biceps brachii	UBERON:0001507	95.80	gold quality
quadriceps femoris	UBERON:0001377	95.74	gold quality
skeletal muscle tissue	UBERON:0001134	95.49	gold quality
muscle of leg	UBERON:0001383	95.12	gold quality
left adrenal gland cortex	UBERON:0035825	93.82	gold quality
right adrenal gland	UBERON:0001233	93.57	gold quality
body of tongue	UBERON:0011876	93.44	gold quality
left adrenal gland	UBERON:0001234	93.39	gold quality
tibialis anterior	UBERON:0001385	93.29	silver quality
right adrenal gland cortex	UBERON:0035827	93.00	gold quality
adrenal cortex	UBERON:0001235	92.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.26	gold quality
muscle tissue	UBERON:0002385	90.27	gold quality
adrenal gland	UBERON:0002369	89.24	gold quality
right testis	UBERON:0004534	89.22	gold quality
deltoid	UBERON:0001476	89.20	gold quality
left testis	UBERON:0004533	88.70	gold quality
testis	UBERON:0000473	85.69	gold quality
tongue	UBERON:0001723	84.46	gold quality
pancreas	UBERON:0001264	84.15	gold quality
right lobe of liver	UBERON:0001114	82.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.03	gold quality
right uterine tube	UBERON:0001302	80.70	gold quality
oocyte	CL:0000023	79.25	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-81547	yes	18.45
E-ANND-3	yes	16.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting TMEM52, 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-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-92B-5P	99.36	63.29	110
HSA-MIR-128-1-5P	99.33	60.46	332
HSA-MIR-128-2-5P	99.33	60.83	311
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-6747-3P	97.73	64.84	1596
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-6762-5P	96.55	64.62	972
HSA-MIR-6845-5P	96.55	64.65	969

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tmem52	ENSMUSG00000023153
rattus_norvegicus	Tmem52	ENSRNOG00000016618

Protein

Protein identifiers

Transmembrane protein 52 — Q8NDY8 (reviewed: Q8NDY8)

All UniProt accessions (4): Q8NDY8, B1AKR2, B1AKR3, R4GMU3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NDY8-1	1	yes
Q8NDY8-2	2

RefSeq proteins (1): NP_848640* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038942	TMEM52	Family

Pfam: PF14979

UniProt features (10 total): compositionally biased region 2, sequence variant 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NDY8-F1	58.98	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): AACTTT_UNKNOWN, AR_01, chr1p36, FOXD2_TARGET_GENES, HHEX_TARGET_GENES, HOXB4_TARGET_GENES, NAB2_TARGET_GENES, SALL4_TARGET_GENES, ZNF322_TARGET_GENES, ZNF610_TARGET_GENES, MIR7110_3P, MIR5695, GSE13306_TREG_RA_VS_TCONV_RA_DN, SAFB2_TARGET_GENES, DESCARTES_MAIN_FETAL_SKELETAL_MUSCLE_CELLS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

362 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM52	GPATCH4	Q5T3I0	595
TMEM52	SINHCAF	Q9NP50	503
TMEM52	ANKRD10	Q9NXR5	489
TMEM52	NXPH4	O95158	480
TMEM52	CFAP74	Q9C0B2	445
TMEM52	STEAP2	Q8NFT2	442
TMEM52	LRRC30	A6NM36	422
TMEM52	CLPSL1	A2RUU4	405
TMEM52	CLSTN2	Q9H4D0	383
TMEM52	ZNF736	B4DX44	380
TMEM52	TMEM120B	A0PK00	370
TMEM52	RPL39L	Q96EH5	369
TMEM52	LRRC14B	A6NHZ5	368
TMEM52	GUCA2A	Q02747	368
TMEM52	LRRC20	Q8TCA0	365

IntAct

4 interactions, top by confidence:

A	B	Type	Score
TMEM52	CALU	psi-mi:“MI:0915”(physical association)	0.400
PCNA	TMEM52	psi-mi:“MI:0915”(physical association)	0.370
VPS35	ILVBL	psi-mi:“MI:0914”(association)	0.350

BioGRID (1): TMEM52 (Proximity Label-MS)

ESM2 similar proteins: A0A1B0GW64, A0A5F4BST2, A0PJX4, A8MVS5, A8MWV9, B0FP48, E5RIL1, E9PGG2, O14836, O60320, O95998, P09564, Q01113, Q01114, Q13477, Q2KI80, Q2T9R2, Q3TS39, Q3UPR0, Q3URD2, Q4V9L6, Q5FVJ4, Q5M869, Q6A044, Q6UWJ8, Q75VT8, Q864V4, Q8BRJ3, Q8BX43, Q8C503, Q8IVY1, Q8K5A9, Q8N112, Q8NC24, Q8NDY8, Q8QZT4, Q8R138, Q969Z4, Q9BUF7, Q9CQM1

Diamond homologs: Q0VBF2, Q4KMG9, Q8NDY8, Q9D702

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

599 predictions. Top by Δscore:

Variant	Effect	Δscore
1:1918160:AGG:A	acceptor_gain	1.0000
1:1918162:GC:G	acceptor_loss	1.0000
1:1918163:C:CC	acceptor_gain	1.0000
1:1918251:A:AC	donor_gain	1.0000
1:1918252:C:CC	donor_gain	1.0000
1:1918252:CAGGT:C	donor_gain	1.0000
1:1919041:TTAC:T	donor_loss	1.0000
1:1919042:TA:T	donor_loss	1.0000
1:1919043:A:AC	donor_gain	1.0000
1:1919043:A:C	donor_loss	1.0000
1:1919044:C:CT	donor_gain	1.0000
1:1919044:CTGGT:C	donor_gain	1.0000
1:1918158:GTAGG:G	acceptor_gain	0.9900
1:1918159:TAGG:T	acceptor_gain	0.9900
1:1918161:GG:G	acceptor_gain	0.9900
1:1918245:GCACT:G	donor_loss	0.9900
1:1918246:CACTC:C	donor_loss	0.9900
1:1918247:AC:A	donor_loss	0.9900
1:1918248:CTCA:C	donor_loss	0.9900
1:1918249:TC:T	donor_loss	0.9900
1:1918250:CACA:C	donor_loss	0.9900
1:1918251:A:C	donor_loss	0.9900
1:1918252:CA:C	donor_gain	0.9900
1:1918252:CAG:C	donor_gain	0.9900
1:1918252:CAGG:C	donor_gain	0.9900
1:1918271:CAGGG:C	donor_gain	0.9900
1:1918394:C:CT	acceptor_gain	0.9900
1:1919038:GACTT:G	donor_loss	0.9900
1:1919039:ACTT:A	donor_loss	0.9900
1:1919044:CT:C	donor_gain	0.9900

AlphaMissense

1311 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:1918397:A:G	C69R	0.961
1:1918913:C:A	W50C	0.960
1:1918913:C:G	W50C	0.960
1:1918393:C:T	G70D	0.950
1:1918901:C:A	W54C	0.943
1:1918901:C:G	W54C	0.943
1:1918903:A:G	W54R	0.939
1:1918903:A:T	W54R	0.939
1:1918915:A:G	W50R	0.938
1:1918915:A:T	W50R	0.938
1:1918263:G:C	S113R	0.937
1:1918263:G:T	S113R	0.937
1:1918265:T:G	S113R	0.937
1:1918379:A:G	C75R	0.936
1:1918394:C:G	G70R	0.923
1:1918275:G:C	S109R	0.922
1:1918275:G:T	S109R	0.922
1:1918277:T:G	S109R	0.922
1:1918155:G:C	S119R	0.913
1:1918155:G:T	S119R	0.913
1:1918157:T:G	S119R	0.913
1:1918402:A:C	L67R	0.913
1:1918894:C:G	G57R	0.909
1:1918894:C:T	G57R	0.909
1:1918414:A:T	V63D	0.889
1:1918423:A:C	L60R	0.889
1:1918405:A:C	L66R	0.875
1:1918429:A:T	L58H	0.874
1:1918390:A:T	V71D	0.873
1:1918408:A:C	L65R	0.871

dbSNP variants (sampled 300 via entrez): RS1000089090 (1:1919967 T>C), RS1000141350 (1:1920183 G>A), RS1000881139 (1:1918708 C>G,T), RS1001147704 (1:1919396 G>A,C,T), RS1001165328 (1:1917354 G>A,C,T), RS1001214542 (1:1917613 C>T), RS1001494352 (1:1919275 A>G), RS1003151755 (1:1917378 T>C), RS1003166679 (1:1921169 G>A), RS1003484657 (1:1919903 A>G), RS1003498216 (1:1920801 G>T), RS1003523799 (1:1920955 C>A,G,T), RS1004000240 (1:1920969 C>G), RS1005060542 (1:1917634 C>G,T), RS1005392139 (1:1919918 T>C)

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

1 associations (top):

Study	Trait	p-value
GCST005951_34	Body mass index	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

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
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
titanium dioxide	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
mono-(2-ethylhexyl)phthalate	decreases methylation, increases abundance	1
butyraldehyde	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
pentanal	increases expression	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	decreases expression, affects binding	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Aldehydes	increases expression	1
Benzo(a)pyrene	affects methylation	1
Camptothecin	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	increases abundance, decreases methylation	1
Estradiol	affects cotreatment, decreases expression	1
Niclosamide	increases expression	1
Phthalic Acids	increases methylation	1

Clinical trials (associated diseases)

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