TMEM200A

Summary

TMEM200A (transmembrane protein 200A, HGNC:21075) is a protein-coding gene on chromosome 6q23.1, encoding Transmembrane protein 200A (Q86VY9).

Predicted to be located in membrane.

Source: NCBI Gene 114801 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 65 total
• MANE Select transcript: NM_001258277

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21075
Approved symbol	TMEM200A
Name	transmembrane protein 200A
Location	6q23.1
Locus type	gene with protein product
Status	Approved
Aliases	TTMC
Ensembl gene	ENSG00000164484
Ensembl biotype	protein_coding
Entrez	114801

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 17 protein_coding

ENST00000296978, ENST00000392429, ENST00000545622, ENST00000617887, ENST00000898610, ENST00000898611, ENST00000898612, ENST00000898613, ENST00000898614, ENST00000898615, ENST00000932435, ENST00000932436, ENST00000932437, ENST00000932438, ENST00000932439, ENST00000952523, ENST00000952524

RefSeq mRNA: 4 — MANE Select: NM_001258277 NM_001258276, NM_001258277, NM_001258278, NM_052913

CCDS: CCDS5140

Canonical transcript exons

ENST00000296978 — 3 exons

Exon	Start	End
ENSE00001084680	130440407	130443067
ENSE00001399499	130385173	130385236
ENSE00001431778	130366017	130366524

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 99.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.6805 / max 447.5521, expressed in 1039 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter ID	TPM avg	Samples expressed
69756	6.5567	860
69758	2.4306	597
69762	2.2570	606
69763	1.1262	454
69760	0.9905	459
69761	0.9142	327
69753	0.6661	455
69754	0.3504	225
69757	0.3497	200
69764	0.2629	153

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.03	gold quality
oocyte	CL:0000023	96.75	gold quality
stromal cell of endometrium	CL:0002255	95.86	gold quality
islet of Langerhans	UBERON:0000006	92.57	gold quality
adrenal tissue	UBERON:0018303	92.42	gold quality
germinal epithelium of ovary	UBERON:0001304	91.20	gold quality
jejunal mucosa	UBERON:0000399	90.64	gold quality
endometrium	UBERON:0001295	89.48	gold quality
visceral pleura	UBERON:0002401	89.00	gold quality
epithelial cell of pancreas	CL:0000083	88.72	gold quality
palpebral conjunctiva	UBERON:0001812	88.47	gold quality
rectum	UBERON:0001052	87.69	gold quality
ileal mucosa	UBERON:0000331	87.36	gold quality
uterus	UBERON:0000995	86.93	gold quality
body of uterus	UBERON:0009853	86.70	gold quality
parietal pleura	UBERON:0002400	86.48	gold quality
myometrium	UBERON:0001296	86.35	gold quality
adrenal gland	UBERON:0002369	86.28	gold quality
mucosa of sigmoid colon	UBERON:0004993	86.19	gold quality
colonic mucosa	UBERON:0000317	86.04	gold quality
right adrenal gland	UBERON:0001233	85.95	gold quality
left adrenal gland	UBERON:0001234	85.92	gold quality
kidney epithelium	UBERON:0004819	85.46	silver quality
left uterine tube	UBERON:0001303	84.91	gold quality
adrenal cortex	UBERON:0001235	84.42	gold quality
left adrenal gland cortex	UBERON:0035825	84.32	gold quality
caput epididymis	UBERON:0004358	84.21	gold quality
right adrenal gland cortex	UBERON:0035827	84.04	gold quality
duodenum	UBERON:0002114	83.47	gold quality
ovary	UBERON:0000992	83.46	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.55

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EZH2

miRNA regulators (miRDB)

105 targeting TMEM200A, 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-1252-5P	100.00	69.80	2774
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509

Literature-anchored findings (GeneRIF, showing 1)

• TMEM200A is a potential prognostic biomarker and correlated with immune infiltrates in gastric cancer. (PMID:37404478)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem200a	ENSDARG00000031540
mus_musculus	Tmem200a	ENSMUSG00000049420
rattus_norvegicus	Tmem200a	ENSRNOG00000047783
drosophila_melanogaster	CG12502	FBGN0035171
caenorhabditis_elegans	R05D7.3	WBGENE00011028

Paralogs (2): TMEM200C (ENSG00000206432), TMEM200B (ENSG00000253304)

Protein

Protein identifiers

Transmembrane protein 200A — Q86VY9 (reviewed: Q86VY9)

All UniProt accessions (2): A8K2A1, Q86VY9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Expressed in cerebellum.

Similarity. Belongs to the TMEM200 family.

RefSeq proteins (4): NP_001245205, NP_001245206, NP_001245207, NP_443145 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018787	DUF2371_TMEM200	Family

Pfam: PF10177

UniProt features (10 total): topological domain 3, transmembrane region 2, chain 1, region of interest 1, compositionally biased region 1, modified residue 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86VY9-F1	52.16	0.05

Functional residue map

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

Post-translational modifications (1): 350

Glycosylation sites (1): 100

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, TTTGTAG_MIR520D, KOYAMA_SEMA3B_TARGETS_UP, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, SABATES_COLORECTAL_ADENOMA_DN, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_UP, MODULE_48, MODULE_95, GEORGES_TARGETS_OF_MIR192_AND_MIR215, chr6q23, SENESE_HDAC1_AND_HDAC2_TARGETS_UP, EPPERT_HSC_R, HORIUCHI_WTAP_TARGETS_UP, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP

GO Biological Process (0):

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

524 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM200A	ALB	P02768	514
TMEM200A	SEBOX	Q9HB31	476
TMEM200A	VMO1	Q7Z5L0	466
TMEM200A	RPL27A	P46776	466
TMEM200A	THEM6	Q8WUY1	459
TMEM200A	TC2N	Q8N9U0	441
TMEM200A	MYH13	Q9UKX3	439
TMEM200A	GABRE	P78334	419
TMEM200A	SAMD3	Q8N6K7	418
TMEM200A	CNOT2	Q9NZN8	413
TMEM200A	MYH8	P13535	407
TMEM200A	ENTREP1	Q15884	403
TMEM200A	FLYWCH2	Q96CP2	402
TMEM200A	GHRH	P01286	401
TMEM200A	OR51I1	Q9H343	397

IntAct

40 interactions, top by confidence:

A	B	Type	Score
PDGFRB	PIK3R2	psi-mi:“MI:0914”(association)	0.610
UNC119	TMEM200A	psi-mi:“MI:0915”(physical association)	0.560
EMD	TMEM200A	psi-mi:“MI:0915”(physical association)	0.560
TMEM200A	BCL2L10	psi-mi:“MI:0915”(physical association)	0.560
SLC31A1	C2orf72	psi-mi:“MI:0914”(association)	0.530
TMEM200A	STX6	psi-mi:“MI:0914”(association)	0.530
KLHDC8A	TCP1	psi-mi:“MI:0914”(association)	0.530
PPP3CC	GSK3A	psi-mi:“MI:0914”(association)	0.530
ANKRD22	ESYT2	psi-mi:“MI:0914”(association)	0.530
KCNE3	RIOK3	psi-mi:“MI:0914”(association)	0.530
TMEM200A	PPP3CB	psi-mi:“MI:0914”(association)	0.530
	SNAP23	psi-mi:“MI:0914”(association)	0.350
TMEM200A	GOSR1	psi-mi:“MI:0914”(association)	0.350
CD81	STX3	psi-mi:“MI:0914”(association)	0.350
CD81	PVR	psi-mi:“MI:0914”(association)	0.350
CD81	CD276	psi-mi:“MI:0914”(association)	0.350
TMEM200A	STX7	psi-mi:“MI:0914”(association)	0.350
PIGH	ILVBL	psi-mi:“MI:0914”(association)	0.350
TMEM9B	NBAS	psi-mi:“MI:0914”(association)	0.350
KCNE3	TMEM131L	psi-mi:“MI:0914”(association)	0.350
TGFBR2	TNFRSF10A	psi-mi:“MI:0914”(association)	0.350
PPP3R2	MAP2K7	psi-mi:“MI:0914”(association)	0.350
BSND	PLD2	psi-mi:“MI:0914”(association)	0.350
INSRR	SETD1A	psi-mi:“MI:0914”(association)	0.350
TMEM268	ABCC4	psi-mi:“MI:0914”(association)	0.350
PCDHGA6	GDF9	psi-mi:“MI:0914”(association)	0.350
CHIA	SLC25A16	psi-mi:“MI:0914”(association)	0.350
DLK1	PLPP3	psi-mi:“MI:0914”(association)	0.350
FYN	MYCBP2	psi-mi:“MI:0914”(association)	0.350

BioGRID (51): TMEM200A (Synthetic Growth Defect), PPP3CC (Affinity Capture-MS), FHOD1 (Affinity Capture-MS), PPP3CB (Affinity Capture-MS), PPP3R1 (Affinity Capture-MS), MYADM (Affinity Capture-MS), STX6 (Affinity Capture-MS), STX10 (Affinity Capture-MS), PPP3CA (Affinity Capture-MS), GOSR1 (Affinity Capture-MS), STX7 (Affinity Capture-MS), TMEM200A (Affinity Capture-MS), TMEM200A (Affinity Capture-MS), TMEM200A (Two-hybrid), TMEM200A (Two-hybrid)

ESM2 similar proteins: A0A1B0GVS7, A2CE83, A2VDU1, A5D992, A8KBE0, O43597, O43609, O43610, P28290, Q02223, Q08AD1, Q08E39, Q14CH0, Q1L0X2, Q2PFN5, Q2TBG9, Q3UUD2, Q4R815, Q5R959, Q5RGQ8, Q5TB30, Q66H35, Q6AYK4, Q6DD45, Q6GPM0, Q6NRB7, Q6P995, Q6PEM6, Q6ZUJ8, Q7ZX27, Q866R9, Q86VY9, Q8BGN6, Q8C3K5, Q8C817, Q8IYD9, Q8N957, Q96HH4, Q9BZD6, Q9C004

Diamond homologs: A6NKL6, Q5RGQ8, Q69YZ2, Q86VY9, Q8C817

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1064 predictions. Top by Δscore:

Variant	Effect	Δscore
6:130440405:A:AG	acceptor_gain	1.0000
6:130440406:G:GG	acceptor_gain	1.0000
6:130440406:GA:G	acceptor_gain	1.0000
6:130365849:G:GT	donor_gain	0.9900
6:130366484:G:GT	donor_gain	0.9900
6:130440402:TTCAG:T	acceptor_gain	0.9900
6:130440403:TCA:T	acceptor_loss	0.9900
6:130440403:TCAG:T	acceptor_gain	0.9900
6:130440404:CAG:C	acceptor_gain	0.9900
6:130440405:AGA:A	acceptor_gain	0.9900
6:130440406:G:GT	acceptor_loss	0.9900
6:130440406:GAG:G	acceptor_gain	0.9900
6:130440406:GAGT:G	acceptor_gain	0.9900
6:130440406:GAGTA:G	acceptor_gain	0.9900
6:130366521:ACAG:A	donor_loss	0.9800
6:130366522:CAGGT:C	donor_loss	0.9800
6:130366523:AG:A	donor_loss	0.9800
6:130366524:GG:G	donor_loss	0.9800
6:130366525:G:A	donor_loss	0.9800
6:130366526:T:A	donor_loss	0.9800
6:130385170:TAGCA:T	acceptor_gain	0.9800
6:130422099:T:TA	donor_gain	0.9800
6:130422100:A:AA	donor_gain	0.9800
6:130440404:CAGA:C	acceptor_gain	0.9800
6:130440405:AGAG:A	acceptor_gain	0.9800
6:130366472:GAC:G	donor_gain	0.9700
6:130367153:A:G	acceptor_gain	0.9700
6:130385171:AGCAC:A	acceptor_gain	0.9700
6:130438707:ATTAC:A	donor_gain	0.9700
6:130440403:TCAGA:T	acceptor_gain	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000038218 (6:130379562 C>A,G,T), RS1000051908 (6:130399829 C>T), RS1000086538 (6:130413012 T>A), RS1000143156 (6:130423012 C>A), RS1000231720 (6:130372771 A>G), RS1000257068 (6:130417226 G>A,C), RS1000289667 (6:130366151 G>A,T), RS1000341350 (6:130402996 G>A), RS1000389750 (6:130366443 C>G,T), RS1000409807 (6:130410183 G>A,C), RS1000433368 (6:130391297 G>A), RS1000509685 (6:130365700 C>T), RS1000510073 (6:130409070 G>T), RS1000540389 (6:130418482 T>C), RS1000579170 (6:130415598 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

4 associations (top):

Study	Trait	p-value
GCST002596_1	Colorectal cancer (calcium intake interaction)	2.000000e-06
GCST003064_6	Exploratory eye movement dysfunction in schizophrenia (cognitive search score)	6.000000e-06
GCST003065_8	Exploratory eye movement dysfunction in schizophrenia (responsive search score)	8.000000e-06
GCST003068_4	Exploratory eye movement dysfunction in schizophrenia (number of eye fixations)	7.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006521	calcium intake measurement
EFO:0007700	exploratory eye movement measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Formaldehyde	decreases expression, increases expression	3
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
Estradiol	affects cotreatment, decreases expression, increases expression	2
Valproic Acid	increases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
methyleugenol	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
mono-(2-ethylhexyl)phthalate	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
tobacco tar	decreases reaction, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
diallyl disulfide	decreases reaction, increases expression	1
hydroquinone	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
2-palmitoylglycerol	increases expression	1
monomethylarsonous acid	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Calcitriol	decreases expression	1
Cisplatin	decreases expression	1
Cytarabine	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Melphalan	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Nickel	increases expression	1
Progesterone	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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