TMEM253

Summary

TMEM253 (transmembrane protein 253, HGNC:32545) is a protein-coding gene on chromosome 14q11.2, encoding Transmembrane protein 253 (P0C7T8).

Predicted to be located in membrane.

Source: NCBI Gene 643382 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_001395467

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32545
Approved symbol	TMEM253
Name	transmembrane protein 253
Location	14q11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000232070
Ensembl biotype	protein_coding
Entrez	643382

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 22 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000418511, ENST00000553744, ENST00000554329, ENST00000554844, ENST00000555314, ENST00000556585, ENST00000673682, ENST00000878425, ENST00000878426, ENST00000878427, ENST00000878428, ENST00000878429, ENST00000878430, ENST00000878431, ENST00000919002, ENST00000919003, ENST00000919004, ENST00000919005, ENST00000919006, ENST00000919007, ENST00000919008, ENST00000919009, ENST00000919010, ENST00000950455, ENST00000950456, ENST00000950457

RefSeq mRNA: 5 — MANE Select: NM_001395467 NM_001146683, NM_001395464, NM_001395465, NM_001395466, NM_001395467

CCDS: CCDS53884

Canonical transcript exons

ENST00000556585 — 7 exons

Exon	Start	End
ENSE00001769524	21103139	21103724
ENSE00002547495	21101865	21101975
ENSE00002550601	21101308	21101451
ENSE00002561892	21102633	21102779
ENSE00003495006	21102405	21102515
ENSE00003662820	21102064	21102120
ENSE00003978133	21101066	21101184

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 97.67.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1034 / max 322.6154, expressed in 462 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
138517	0.7480	432
138519	0.2002	13
138518	0.1552	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
duodenum	UBERON:0002114	97.67	gold quality
mucosa of transverse colon	UBERON:0004991	94.61	gold quality
small intestine Peyer’s patch	UBERON:0003454	87.06	gold quality
small intestine	UBERON:0002108	86.37	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.33	gold quality
rectum	UBERON:0001052	84.05	gold quality
transverse colon	UBERON:0001157	80.96	gold quality
left lobe of thyroid gland	UBERON:0001120	75.45	gold quality
intestine	UBERON:0000160	75.44	gold quality
right lobe of thyroid gland	UBERON:0001119	75.33	gold quality
thyroid gland	UBERON:0002046	75.22	gold quality
right adrenal gland cortex	UBERON:0035827	71.71	gold quality
right adrenal gland	UBERON:0001233	71.64	gold quality
colon	UBERON:0001155	71.49	gold quality
saliva-secreting gland	UBERON:0001044	71.25	gold quality
left adrenal gland	UBERON:0001234	70.55	gold quality
left adrenal gland cortex	UBERON:0035825	70.49	gold quality
minor salivary gland	UBERON:0001830	70.30	gold quality
lower esophagus mucosa	UBERON:0035834	69.29	gold quality
adrenal gland	UBERON:0002369	68.15	gold quality
esophagus mucosa	UBERON:0002469	63.92	gold quality
body of pancreas	UBERON:0001150	62.75	gold quality
right lobe of liver	UBERON:0001114	62.54	gold quality
gall bladder	UBERON:0002110	62.47	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	62.46	gold quality
smooth muscle tissue	UBERON:0001135	62.19	gold quality
placenta	UBERON:0001987	62.13	gold quality
skin of abdomen	UBERON:0001416	61.21	gold quality
vermiform appendix	UBERON:0001154	61.07	gold quality
zone of skin	UBERON:0000014	61.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting TMEM253, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-936	98.87	70.51	1124
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-12114	98.70	63.45	730
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-5089-5P	98.45	66.06	1388
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-6730-5P	98.03	68.12	1299
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-6783-5P	97.67	67.21	1528
HSA-MIR-12128	96.67	66.98	1471

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tmem253	ENSMUSG00000072571
rattus_norvegicus	Tmem253	ENSRNOG00000039489

Protein

Protein identifiers

Transmembrane protein 253 — P0C7T8 (reviewed: P0C7T8)

All UniProt accessions (3): A0A669KB37, P0C7T8, H0YLA3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (5): NP_001140155, NP_001382393, NP_001382394, NP_001382395, NP_001382396* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038874	TMEM253	Family

UniProt features (6 total): transmembrane region 4, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7T8-F1	72.39	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): KOHOUTEK_CCNT2_TARGETS, DELACROIX_RAR_BOUND_ES, GSE13522_WT_VS_IFNG_KO_SKIN_UP, KMT2D_TARGET_GENES, NKX2_3_TARGET_GENES, SUPT16H_TARGET_GENES, ZNF664_TARGET_GENES, MIR5196_5P, MIR4747_5P, MIR6783_3P, MIR1343_3P, MIR7854_3P, MIR4710, MIR8071, BUSSLINGER_DUODENAL_MATURE_ENTEROCYTES

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

130 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM253	TMEM151B	Q8IW70	621
TMEM253	TMEM151A	Q8N4L1	615
TMEM253	WDR49	Q8IV35	583
TMEM253	NOXRED1	Q6NXP6	580
TMEM253	TMEM50A	O95807	545
TMEM253	ARFGEF3	Q5TH69	541
TMEM253	OR2Z1	Q8NG97	541
TMEM253	TMEM116	Q8NCL8	540
TMEM253	TRMO	Q9BU70	506
TMEM253	SLC6A16	Q9GZN6	479
TMEM253	ZNF804B	A4D1E1	476
TMEM253	FAM162B	Q5T6X4	475
TMEM253	SLC10A5	Q5PT55	475
TMEM253	FER1L5	A0AVI2	448
TMEM253	PCNX2	A6NKB5	447

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RAPGEF5	TMEM253	psi-mi:“MI:0915”(physical association)	0.370
TMEM253	TUBA1B	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (2): RAPGEF5 (Two-hybrid), TUBA1B (Two-hybrid)

ESM2 similar proteins: A0A1B0GUA5, A0A286YF58, A0A2R8YCJ5, A0JNN8, A2A699, A2AEV7, A2ARS0, A2VDX9, A5PJP1, A6NGB7, A6NKF7, A6QQ91, A8MVW0, C9JTQ0, F1MUS9, G3MZC5, O95996, P0C7T8, P0DPE3, P46062, P98162, Q0II74, Q0VD38, Q14761, Q1LZC5, Q29RK8, Q2HJ59, Q2VPB7, Q2VPJ9, Q3TAP4, Q3TYP4, Q566C8, Q64322, Q64697, Q6F5E0, Q6ZS72, Q7M733, Q7TN12, Q86YV0, Q86YV9

Diamond homologs: P0C7T8, Q0II74, Q3UNB8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1283 predictions. Top by Δscore:

Variant	Effect	Δscore
14:21101976:G:GG	donor_gain	1.0000
14:21102777:G:GT	donor_gain	1.0000
14:21101414:C:T	donor_gain	0.9900
14:21102059:TTCAG:T	acceptor_loss	0.9900
14:21102060:TCA:T	acceptor_loss	0.9900
14:21102061:CA:C	acceptor_loss	0.9900
14:21102062:A:AC	acceptor_loss	0.9900
14:21102129:G:T	donor_gain	0.9900
14:21102190:G:GT	donor_gain	0.9900
14:21102193:G:GG	donor_gain	0.9900
14:21102446:G:A	acceptor_gain	0.9900
14:21102453:ATAGT:A	acceptor_gain	0.9900
14:21102455:A:AG	acceptor_gain	0.9900
14:21102455:AGT:A	acceptor_gain	0.9900
14:21102456:G:GG	acceptor_gain	0.9900
14:21102456:GTG:G	acceptor_gain	0.9900
14:21102776:GGAG:G	donor_gain	0.9900
14:21102793:G:T	donor_gain	0.9900
14:21103135:TCAG:T	acceptor_loss	0.9900
14:21103136:CAG:C	acceptor_loss	0.9900
14:21103137:A:AC	acceptor_loss	0.9900
14:21103137:A:AG	acceptor_gain	0.9900
14:21103138:G:GG	acceptor_gain	0.9900
14:21102062:A:AG	acceptor_gain	0.9800
14:21102062:AG:A	acceptor_gain	0.9800
14:21102063:G:GG	acceptor_gain	0.9800
14:21102063:GG:G	acceptor_gain	0.9800
14:21102631:A:AG	acceptor_gain	0.9800
14:21102632:G:GG	acceptor_gain	0.9800
14:21102632:GC:G	acceptor_gain	0.9800

AlphaMissense

1385 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:21102428:C:A	N100K	0.968
14:21102428:C:G	N100K	0.968
14:21101877:T:A	W41R	0.966
14:21101877:T:C	W41R	0.966
14:21101868:A:C	S38R	0.964
14:21101870:C:A	S38R	0.964
14:21101870:C:G	S38R	0.964
14:21102660:A:C	S139R	0.955
14:21102662:T:A	S139R	0.955
14:21102662:T:G	S139R	0.955
14:21101412:G:C	W23C	0.948
14:21101412:G:T	W23C	0.948
14:21102120:G:C	K92N	0.942
14:21102120:G:T	K92N	0.942
14:21102077:G:A	G78E	0.927
14:21102076:G:A	G78R	0.926
14:21102076:G:C	G78R	0.926
14:21102095:T:C	L84P	0.922
14:21101919:T:C	C55R	0.916
14:21102083:T:A	V80D	0.912
14:21102447:G:C	G107R	0.909
14:21101899:C:G	P48R	0.899
14:21102095:T:A	L84H	0.899
14:21102064:G:C	G74R	0.895
14:21102416:G:A	M96I	0.894
14:21102416:G:C	M96I	0.894
14:21102416:G:T	M96I	0.894
14:21102076:G:T	G78W	0.888
14:21102415:T:A	M96K	0.879
14:21101450:C:A	A36E	0.877

dbSNP variants (sampled 300 via entrez): RS1000157852 (14:21099224 A>G), RS1000195848 (14:21101178 A>C), RS1000510519 (14:21098894 C>T), RS1000630471 (14:21097343 C>CATGGGGGGG), RS1000708801 (14:21103235 C>T), RS1000739889 (14:21102860 G>A,T), RS1001006640 (14:21097995 A>C), RS1001110199 (14:21100789 C>T), RS1002262001 (14:21103636 T>C,G), RS1003104393 (14:21098016 C>A,G,T), RS1003544940 (14:21097794 CAA>C), RS1003609313 (14:21097808 C>A), RS1003661457 (14:21098776 C>A,T), RS1004578979 (14:21098709 A>G), RS1004609812 (14:21098438 C>A,T)

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

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
1,6-hexamethylene diisocyanate	increases methylation	1
ferrous chloride	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
perfluorooctane sulfonic acid	increases expression	1
jinfukang	affects cotreatment, increases expression	1
2,6-dichloro-(1,4)benzoquinone	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Urethane	decreases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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