TMEM204

Summary

TMEM204 (transmembrane protein 204, HGNC:14158) is a protein-coding gene on chromosome 16p13.3, encoding Transmembrane protein 204 (Q9BSN7). Can influence paracellular permeability.

C16ORF30 plays a role in cell adhesion and cellular permeability at adherens junctions (Kearsey et al., 2004 [PubMed 15206924]).

Source: NCBI Gene 79652 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_024600

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14158
Approved symbol	TMEM204
Name	transmembrane protein 204
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20898, CLP24
Ensembl gene	ENSG00000131634
Ensembl biotype	protein_coding
OMIM	611002
Entrez	79652

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000253934, ENST00000566264, ENST00000889470

RefSeq mRNA: 2 — MANE Select: NM_024600 NM_001256541, NM_024600

CCDS: CCDS42098

Canonical transcript exons

ENST00000566264 — 3 exons

Exon	Start	End
ENSE00001164129	1541921	1542076
ENSE00002620465	1533666	1534555
ENSE00003841403	1554782	1555568

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 97.03.

FANTOM5 (CAGE): breadth broad, TPM avg 6.4437 / max 122.6690, expressed in 859 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152108	6.0041	851
152107	0.4294	269
152106	0.0102	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lung	UBERON:0002167	97.03	gold quality
apex of heart	UBERON:0002098	96.03	gold quality
lower lobe of lung	UBERON:0008949	95.13	gold quality
upper lobe of left lung	UBERON:0008952	94.86	gold quality
upper lobe of lung	UBERON:0008948	94.82	gold quality
ascending aorta	UBERON:0001496	94.62	gold quality
thoracic aorta	UBERON:0001515	94.55	gold quality
right lobe of thyroid gland	UBERON:0001119	94.50	gold quality
descending thoracic aorta	UBERON:0002345	94.11	gold quality
left coronary artery	UBERON:0001626	93.92	gold quality
metanephros cortex	UBERON:0010533	93.39	gold quality
coronary artery	UBERON:0001621	93.26	gold quality
omental fat pad	UBERON:0010414	92.41	gold quality
aorta	UBERON:0000947	92.38	gold quality
peritoneum	UBERON:0002358	92.37	gold quality
left lobe of thyroid gland	UBERON:0001120	92.35	gold quality
adipose tissue of abdominal region	UBERON:0007808	92.21	gold quality
heart left ventricle	UBERON:0002084	92.14	gold quality
cardiac ventricle	UBERON:0002082	92.07	gold quality
mucosa of stomach	UBERON:0001199	91.92	gold quality
thyroid gland	UBERON:0002046	91.24	gold quality
subcutaneous adipose tissue	UBERON:0002190	91.23	gold quality
lung	UBERON:0002048	91.10	gold quality
right coronary artery	UBERON:0001625	90.99	gold quality
lower esophagus muscularis layer	UBERON:0035833	90.97	gold quality
lower esophagus	UBERON:0013473	90.87	gold quality
tibial artery	UBERON:0007610	90.85	gold quality
popliteal artery	UBERON:0002250	90.83	gold quality
right atrium auricular region	UBERON:0006631	90.78	gold quality
heart	UBERON:0000948	90.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting TMEM204, 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-3120-5P	100.00	65.56	965
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-6830-5P	99.01	68.73	1884
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-4752	98.71	68.04	833
HSA-MIR-376B-5P	98.46	66.40	606
HSA-MIR-376C-5P	98.46	66.64	589
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-345-5P	96.40	66.43	663
HSA-MIR-4749-3P	96.40	66.24	798

Literature-anchored findings (GeneRIF, showing 1)

• suggests that CLP24 is a novel, hypoxically regulated tetraspan adherens junction protein that modulates cell adhesion, paracellular permeability and angiogenesis (PMID:15206924)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem204	ENSDARG00000045273
mus_musculus	Tmem204	ENSMUSG00000024168
rattus_norvegicus	Tmem204	ENSRNOG00000016494

Protein

Protein identifiers

Transmembrane protein 204 — Q9BSN7 (reviewed: Q9BSN7)

Alternative names: Claudin-like protein 24

All UniProt accessions (1): Q9BSN7

UniProt curated annotations — full annotation on UniProt →

Function. Can influence paracellular permeability. Appears to be involved in cell-cell interactions through adherens.

Subcellular location. Cell junction. Adherens junction. Cell membrane.

Tissue specificity. Highly expressed in lung, heart, kidney and placenta. Lower expression in thymus, spleen, liver, testis and ovary. Expressed in endothelial and restricted epithelial cell populations.

Induction. By hypoxia.

RefSeq proteins (2): NP_001243470, NP_078876* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038992	TMEM204	Family

UniProt features (12 total): topological domain 5, transmembrane region 4, chain 1, glycosylation site 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSN7-F1	70.99	0.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 164

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 138 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_SMOOTH_MUSCLE_CELL_DIFFERENTIATION, GOBP_VASCULAR_ENDOTHELIAL_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, FOXO4_01, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_REGULATION_OF_VASCULAR_ENDOTHELIAL_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, LYF1_01, GOBP_RESPONSE_TO_GROWTH_FACTOR, RYTTCCTG_ETS2_B, HAND1E47_01, CUI_TCF21_TARGETS_2_DN, GOCC_CELL_CELL_JUNCTION

GO Biological Process (3): lymph vessel development (GO:0001945), regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947), smooth muscle cell differentiation (GO:0051145)

GO Molecular Function (0):

GO Cellular Component (4): plasma membrane (GO:0005886), adherens junction (GO:0005912), membrane (GO:0016020), anchoring junction (GO:0070161)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
vasculature development	1
anatomical structure development	1
regulation of signal transduction	1
vascular endothelial growth factor receptor signaling pathway	1
regulation of cellular response to growth factor stimulus	1
muscle cell differentiation	1
membrane	1
cell periphery	1
cell-cell junction	1
cellular anatomical structure	1
cell junction	1

Protein interactions and networks

STRING

846 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM204	ATR	Q13535	760
TMEM204	KIAA1143	Q96AT1	721
TMEM204	KDR	P35968	684
TMEM204	TJP1	Q07157	596
TMEM204	FLT4	P35916	549
TMEM204	SAMSN1	Q9NSI8	509
TMEM204	CRTAM	O95727	485
TMEM204	KBTBD12	Q3ZCT8	481
TMEM204	IFT140	Q96RY7	470
TMEM204	TMEM178A	Q8NBL3	469
TMEM204	IHO1	Q8IYA8	441
TMEM204	GIMAP7	Q8NHV1	422
TMEM204	CXCR3	P49682	422
TMEM204	RRP36	Q96EU6	415
TMEM204	KCNG3	Q8TAE7	412

IntAct

2 interactions, top by confidence:

A	B	Type	Score
TMEM204	STX10	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): TMEM204 (Positive Genetic), SLC12A7 (Affinity Capture-MS), STX10 (Affinity Capture-MS), DCAKD (Affinity Capture-MS), FYN (Affinity Capture-MS), AXL (Affinity Capture-MS), BMPR1A (Affinity Capture-MS), CIB1 (Affinity Capture-MS), OSMR (Affinity Capture-MS), TMEM204 (Negative Genetic), TMEM204 (PCA), TMEM204 (PCA)

ESM2 similar proteins: A6NFC5, A6NM45, A8MUP6, B1AQL3, C3VMW3, C9JDP6, O35912, O75204, O88551, O88552, O95500, O95832, P56745, P56746, P56748, P56750, P57739, Q08DE1, Q0V9E0, Q0VCN0, Q16617, Q2KIY2, Q2KJ11, Q3UUA0, Q4V922, Q5CZV0, Q5M962, Q5QT56, Q6ICI0, Q765P1, Q7T392, Q7TQI0, Q7Z7N9, Q8BGP5, Q8BXA6, Q8N7P3, Q8NHS1, Q8VHW3, Q95KM6, Q96B33

Diamond homologs: Q0IIE5, Q5M962, Q7TQI0, Q9BSN7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1617 predictions. Top by Δscore:

Variant	Effect	Δscore
16:1541911:T:TA	acceptor_gain	1.0000
16:1541919:A:AG	acceptor_gain	1.0000
16:1541920:G:GG	acceptor_gain	1.0000
16:1541920:GT:G	acceptor_gain	1.0000
16:1541920:GTGC:G	acceptor_gain	1.0000
16:1541920:GTGCA:G	acceptor_gain	1.0000
16:1542073:GCGA:G	donor_gain	1.0000
16:1542074:CGA:C	donor_gain	1.0000
16:1542074:CGAGT:C	donor_loss	1.0000
16:1542075:GA:G	donor_gain	1.0000
16:1542075:GAG:G	donor_gain	1.0000
16:1542077:G:GG	donor_gain	1.0000
16:1542077:GTAA:G	donor_loss	1.0000
16:1542078:TAA:T	donor_loss	1.0000
16:1528794:CCGG:C	donor_loss	0.9900
16:1528795:CGGT:C	donor_loss	0.9900
16:1528797:GT:G	donor_loss	0.9900
16:1528798:T:A	donor_loss	0.9900
16:1541912:G:A	acceptor_gain	0.9900
16:1541915:CCACA:C	acceptor_loss	0.9900
16:1541918:CAG:C	acceptor_loss	0.9900
16:1541919:AGT:A	acceptor_gain	0.9900
16:1541919:AGTGC:A	acceptor_loss	0.9900
16:1541920:GTG:G	acceptor_gain	0.9900
16:1542079:AA:A	donor_loss	0.9900
16:1554774:A:AG	acceptor_gain	0.9900
16:1554775:T:G	acceptor_gain	0.9900
16:1554779:CA:C	acceptor_loss	0.9900
16:1554780:A:AG	acceptor_gain	0.9900
16:1554781:G:GA	acceptor_gain	0.9900

AlphaMissense

1440 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:1541926:T:C	F96L	0.997
16:1541928:C:A	F96L	0.997
16:1541928:C:G	F96L	0.997
16:1534365:G:C	W30C	0.996
16:1534365:G:T	W30C	0.996
16:1541949:C:A	N103K	0.996
16:1541949:C:G	N103K	0.996
16:1542064:T:C	F142L	0.996
16:1542065:T:C	F142S	0.996
16:1542066:C:A	F142L	0.996
16:1542066:C:G	F142L	0.996
16:1554799:G:A	G152R	0.996
16:1554799:G:C	G152R	0.996
16:1541978:G:A	G113D	0.995
16:1554811:T:C	F156L	0.995
16:1554813:C:A	F156L	0.995
16:1554813:C:G	F156L	0.995
16:1554871:T:C	C176R	0.995
16:1534338:C:A	N21K	0.994
16:1534338:C:G	N21K	0.994
16:1541927:T:G	F96C	0.994
16:1541957:C:A	A106D	0.994
16:1541969:T:C	L110P	0.994
16:1534413:G:C	W46C	0.993
16:1534413:G:T	W46C	0.993
16:1534509:G:C	W78C	0.993
16:1534509:G:T	W78C	0.993
16:1541969:T:A	L110H	0.993
16:1554799:G:T	G152W	0.993
16:1554800:G:A	G152E	0.993

dbSNP variants (sampled 300 via entrez): RS1000032230 (16:1537767 G>A), RS1000054839 (16:1550499 G>C,T), RS1000084062 (16:1537923 G>T), RS1000194311 (16:1535011 C>A), RS1000250067 (16:1533725 G>A), RS1000355970 (16:1551768 C>T), RS1000435978 (16:1546424 G>A), RS1000438764 (16:1546596 C>T), RS1000509561 (16:1527285 G>C), RS1000523282 (16:1545209 C>T), RS1000549905 (16:1553757 G>A), RS1000607652 (16:1549041 T>G), RS1000618234 (16:1542174 C>A,G,T), RS1000785479 (16:1527086 C>G,T), RS1000802591 (16:1540074 C>A)

Disease associations

OMIM: gene MIM:611002 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002949_19	Epilepsy and lamotrigine-induced maculopapular eruptions	3.000000e-10
GCST005194_188	Coronary artery disease	8.000000e-06
GCST010866_66	Coronary artery disease	3.000000e-08
GCST90000025_250	Appendicular lean mass	2.000000e-12

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:1001253	maculopapular eruption
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	2
pirinixic acid	affects binding, decreases expression, increases activity	1
butyraldehyde	increases expression	1
di-n-butylphosphoric acid	affects expression	1
mono(2-ethyl-5-oxohexyl)phthalate	increases abundance, increases methylation	1
mono(2-ethyl-5-hydroxyhexyl) phthalate	increases abundance, increases methylation	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
mono-isobutyl phthalate	increases abundance, increases methylation	1
Catechin	affects cotreatment, increases expression	1
Dexamethasone	decreases expression	1
Phthalic Acids	increases abundance, increases methylation	1
Progesterone	increases expression	1
Smoke	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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