TMEM130

Summary

TMEM130 (transmembrane protein 130, HGNC:25429) is a protein-coding gene on chromosome 7q22.1, encoding Transmembrane protein 130 (Q8N3G9).

Located in Golgi apparatus.

Source: NCBI Gene 222865 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 68 total
• MANE Select transcript: NM_152913

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25429
Approved symbol	TMEM130
Name	transmembrane protein 130
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761L1417, FLJ42643
Ensembl gene	ENSG00000166448
Ensembl biotype	protein_coding
Entrez	222865

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000339375, ENST00000345589, ENST00000416379, ENST00000445790, ENST00000450876, ENST00000461092, ENST00000474857, ENST00000486839, ENST00000879709

RefSeq mRNA: 3 — MANE Select: NM_152913 NM_001134450, NM_001134451, NM_152913

CCDS: CCDS47649, CCDS47650, CCDS5658

Canonical transcript exons

ENST00000339375 — 8 exons

Exon	Start	End
ENSE00001905958	98869777	98870014
ENSE00002437595	98846490	98848208
ENSE00002496838	98851421	98851623
ENSE00002497306	98848583	98848695
ENSE00002525255	98860179	98860338
ENSE00003499163	98856017	98856183
ENSE00003543822	98863095	98863400
ENSE00003608867	98855240	98855324

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 97.85.

FANTOM5 (CAGE): breadth broad, TPM avg 8.8854 / max 535.7839, expressed in 336 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85073	4.4316	198
85074	3.0166	247
85072	0.6221	90
85060	0.3683	96
85059	0.1519	43
85063	0.0694	34
85058	0.0535	28
85069	0.0498	28
85062	0.0311	16
85068	0.0306	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 9	UBERON:0013540	97.85	gold quality
prefrontal cortex	UBERON:0000451	97.74	gold quality
nucleus accumbens	UBERON:0001882	97.63	gold quality
right frontal lobe	UBERON:0002810	97.58	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.40	gold quality
hypothalamus	UBERON:0001898	97.25	gold quality
frontal cortex	UBERON:0001870	97.05	gold quality
anterior cingulate cortex	UBERON:0009835	97.00	gold quality
neocortex	UBERON:0001950	96.07	gold quality
amygdala	UBERON:0001876	96.04	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.03	gold quality
caudate nucleus	UBERON:0001873	95.77	gold quality
putamen	UBERON:0001874	95.70	gold quality
cerebral cortex	UBERON:0000956	95.64	gold quality
pituitary gland	UBERON:0000007	95.48	gold quality
Ammon’s horn	UBERON:0001954	95.36	gold quality
superior frontal gyrus	UBERON:0002661	95.33	gold quality
forebrain	UBERON:0001890	95.23	gold quality
temporal lobe	UBERON:0001871	95.18	gold quality
right coronary artery	UBERON:0001625	94.96	gold quality
adenohypophysis	UBERON:0002196	94.82	gold quality
substantia nigra pars compacta	UBERON:0001965	94.67	gold quality
brain	UBERON:0000955	94.57	gold quality
parietal lobe	UBERON:0001872	94.57	gold quality
entorhinal cortex	UBERON:0002728	94.46	gold quality
postcentral gyrus	UBERON:0002581	94.41	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.75	gold quality
cerebellar cortex	UBERON:0002129	93.71	gold quality
superior vestibular nucleus	UBERON:0007227	93.71	gold quality
cerebellar hemisphere	UBERON:0002245	93.68	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-84465	yes	1207.76
E-GEOD-81547	yes	4.70
E-ANND-3	yes	3.39
E-MTAB-6379	no	17.32
E-GEOD-99795	no	2.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting TMEM130, 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-6867-5P	100.00	82.21	3464
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-205-3P	99.92	69.92	3165
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-3177-5P	99.65	70.38	1174
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-365A-3P	99.43	70.02	836
HSA-MIR-365B-3P	99.43	70.02	836
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-4641	99.28	66.64	744
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-877-3P	99.09	68.10	1637
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-1246	98.54	66.21	959
HSA-MIR-4712-3P	98.52	65.39	822

Literature-anchored findings (GeneRIF, showing 3)

• The promoter aberrant methylation status of TMEM130 is associated with gastric cancer. (PMID:34162508)
• Functional Domains and Evolutionary History of the PMEL and GPNMB Family Proteins. (PMID:34207849)
• DNA methylation-mediated down-regulation of TMEM130 promotes cell migration in breast cancer. (PMID:34763116)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem130	ENSDARG00000103789
mus_musculus	Tmem130	ENSMUSG00000043388
rattus_norvegicus	Tmem130	ENSRNOG00000025235

Paralogs (2): GPNMB (ENSG00000136235), PMEL (ENSG00000185664)

Protein

Protein identifiers

Transmembrane protein 130 — Q8N3G9 (reviewed: Q8N3G9)

All UniProt accessions (3): C9JQV5, G3V0E7, Q8N3G9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Golgi apparatus membrane.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N3G9-1	1	yes
Q8N3G9-2	2
Q8N3G9-3	3

RefSeq proteins (3): NP_001127922, NP_001127923, NP_690877* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000601	PKD_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR035986	PKD_dom_sf	Homologous_superfamily
IPR045219	PKAT	Family
IPR046846	PKAT_KLD	Domain

Pfam: PF20433

UniProt features (14 total): glycosylation site 3, splice variant 2, sequence conflict 2, topological domain 2, signal peptide 1, chain 1, sequence variant 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N3G9-F1	79.13	0.53

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 (3): 34, 197, 300

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): LIU_SMARCA4_TARGETS, MIKKELSEN_NPC_HCP_WITH_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, MARTENS_TRETINOIN_RESPONSE_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, CSR_LATE_UP.V1_UP, ZNF423_TARGET_GENES, ZNF563_TARGET_GENES, ZNF667_TARGET_GENES, MIR6867_5P, MIR141_3P, MIR200A_3P, LET_7A_2_3P, LET_7G_3P, MIR3145_3P

GO Biological Process (0):

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

GO Cellular Component (4): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1612 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM130	UBE2QL1	A1L167	473
TMEM130	B3GALT2	O43825	419
TMEM130	TMEM278	A6NKF7	379
TMEM130	TMEM145	Q8NBT3	372
TMEM130	CFAP144	A6NL82	370
TMEM130	NPTX2	P47972	367
TMEM130	PGM2L1	Q6PCE3	365
TMEM130	GRID2IP	A4D2P6	364
TMEM130	ENTREP2	O60320	363
TMEM130	ZNF521	Q96K83	361
TMEM130	C12orf43	Q96C57	360
TMEM130	TMEM179	Q6ZVK1	354
TMEM130	FAM81A	Q8TBF8	348
TMEM130	UNC80	Q8N2C7	346
TMEM130	CGREF1	Q99674	345
TMEM130	DCUN1D4	Q92564	345

IntAct

33 interactions, top by confidence:

A	B	Type	Score
OLFM4	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
NKG7	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
PIGF	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
MFSD5	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
SLC2A5	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
TSPAN2	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
GRM2	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
TMEM130	YIPF6	psi-mi:“MI:0915”(physical association)	0.560
TMEM130	SLC35B4	psi-mi:“MI:0915”(physical association)	0.560
TMEM130	TMEM100	psi-mi:“MI:0915”(physical association)	0.560
TMEM130	GOLIM4	psi-mi:“MI:0914”(association)	0.350
GIP	GNPAT	psi-mi:“MI:0914”(association)	0.350
MFSD5	TMEM130	psi-mi:“MI:0915”(physical association)	0.000
TMEM130	SLC2A5	psi-mi:“MI:0915”(physical association)	0.000
SLC35B4	TMEM130	psi-mi:“MI:0915”(physical association)	0.000
SLC2A5	TMEM130	psi-mi:“MI:0915”(physical association)	0.000
TSPAN2	TMEM130	psi-mi:“MI:0915”(physical association)	0.000
GRM2	TMEM130	psi-mi:“MI:0915”(physical association)	0.000
TMEM100	TMEM130	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (35): TMEM130 (Two-hybrid), TMEM130 (Two-hybrid), TMEM130 (Two-hybrid), TMEM130 (Two-hybrid), TMEM130 (Two-hybrid), TMEM130 (Two-hybrid), TMEM130 (Two-hybrid), YIPF6 (Two-hybrid), MFSD5 (Two-hybrid), SLC35B4 (Two-hybrid), FAM20B (Affinity Capture-MS), POM121 (Affinity Capture-MS), TMEM130 (Affinity Capture-MS), TMEM131 (Affinity Capture-MS), TNPO3 (Affinity Capture-MS)

ESM2 similar proteins: A0A8M9PDM1, A2RU67, B8JI67, D3YX43, D3ZWJ9, E1B9E5, O08721, O08722, O60486, P35054, P35916, P35917, Q2HJE5, Q3TYX2, Q5F3L3, Q5M7W6, Q5R6F5, Q62190, Q63961, Q6AXW8, Q6NXM3, Q6P7C7, Q6PVW7, Q6ZN44, Q6ZQQ6, Q76MJ5, Q7TN88, Q80VA5, Q86XM0, Q8BYI8, Q8C0Z1, Q8CB67, Q8IZJ1, Q8K1S3, Q8K1S4, Q8N3G9, Q8TF17, Q8VI51, Q8WY21, Q91ZT1

Diamond homologs: Q5R6F5, Q6NXM3, Q8N3G9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1507 predictions. Top by Δscore:

Variant	Effect	Δscore
7:98848579:CCA:C	donor_loss	1.0000
7:98848581:A:AT	donor_loss	1.0000
7:98848582:C:CT	donor_loss	1.0000
7:98855236:TTAC:T	donor_loss	1.0000
7:98855237:TAC:T	donor_loss	1.0000
7:98855238:A:AC	donor_gain	1.0000
7:98855238:A:C	donor_loss	1.0000
7:98855238:ACCT:A	donor_gain	1.0000
7:98855238:ACCTC:A	donor_gain	1.0000
7:98855239:C:CC	donor_gain	1.0000
7:98855239:CCT:C	donor_gain	1.0000
7:98855239:CCTC:C	donor_gain	1.0000
7:98855239:CCTCC:C	donor_gain	1.0000
7:98855320:GGTTT:G	acceptor_gain	1.0000
7:98855321:GTTT:G	acceptor_gain	1.0000
7:98855322:TTT:T	acceptor_gain	1.0000
7:98855323:TT:T	acceptor_gain	1.0000
7:98855324:TCTG:T	acceptor_loss	1.0000
7:98855325:C:CA	acceptor_loss	1.0000
7:98855325:C:CC	acceptor_gain	1.0000
7:98855326:T:A	acceptor_loss	1.0000
7:98856012:CCCA:C	donor_loss	1.0000
7:98856014:CACC:C	donor_loss	1.0000
7:98856015:AC:A	donor_gain	1.0000
7:98856016:C:CG	donor_loss	1.0000
7:98856016:CC:C	donor_gain	1.0000
7:98856016:CCCTG:C	donor_gain	1.0000
7:98856184:C:G	acceptor_loss	1.0000
7:98856185:T:A	acceptor_loss	1.0000
7:98860174:CCTA:C	donor_loss	1.0000

AlphaMissense

2759 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:98860195:A:G	W179R	0.991
7:98860195:A:T	W179R	0.991
7:98848666:A:G	C346R	0.988
7:98863266:A:G	W74R	0.986
7:98863266:A:T	W74R	0.986
7:98860193:C:A	W179C	0.985
7:98860193:C:G	W179C	0.985
7:98863264:C:A	W74C	0.982
7:98863264:C:G	W74C	0.982
7:98863270:G:C	F72L	0.982
7:98863270:G:T	F72L	0.982
7:98863272:A:G	F72L	0.982
7:98848662:G:T	A347D	0.980
7:98851562:A:G	C289R	0.980
7:98851586:A:G	C281R	0.977
7:98856112:A:G	L208P	0.973
7:98860327:C:A	G135W	0.973
7:98848659:G:T	T348K	0.972
7:98851491:G:C	C312W	0.971
7:98851493:A:G	C312R	0.971
7:98856039:G:C	F232L	0.968
7:98856039:G:T	F232L	0.968
7:98856041:A:G	F232L	0.968
7:98851478:C:G	A317P	0.966
7:98863271:A:G	F72S	0.966
7:98860326:C:T	G135E	0.964
7:98848638:G:T	A355D	0.962
7:98848674:G:T	A343D	0.962
7:98860194:C:G	W179S	0.962
7:98863172:A:T	V105D	0.962

dbSNP variants (sampled 300 via entrez): RS1000641213 (7:98871006 C>G,T), RS1000823276 (7:98855776 G>A), RS1000838803 (7:98861823 A>G), RS1000986966 (7:98866827 A>G), RS1001405606 (7:98846647 C>T), RS1001413591 (7:98846425 A>C), RS1001717114 (7:98857177 C>A), RS1001812104 (7:98856977 G>A), RS1001881044 (7:98862888 C>T), RS1002012725 (7:98852025 C>T), RS1002025612 (7:98867758 A>G), RS1002271347 (7:98863022 T>C), RS1002333324 (7:98862737 C>A,T), RS1002408452 (7:98847848 G>T), RS1002418299 (7:98847542 G>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

1 associations (top):

Study	Trait	p-value
GCST009560_2	Decreased low contrast letter acuity in multiple sclerosis	7.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008385	visual acuity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1203844	TMEM130		0.00	0

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	5
Arsenic Trioxide	decreases reaction, decreases expression, affects binding	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
propionaldehyde	increases expression	1
trichostatin A	decreases expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
pentanal	increases expression	1
entinostat	increases expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Vehicle Emissions	increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Cadmium	decreases expression, increases abundance	1
Estradiol	affects cotreatment, decreases expression	1
Lead	affects expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Palmitic Acid	increases expression	1

Clinical trials (associated diseases)

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