TVP23A

Summary

TVP23A (trans-golgi network vesicle protein 23 homolog A, HGNC:20398) is a protein-coding gene on chromosome 16p13.13, encoding Golgi apparatus membrane protein TVP23 homolog A (A6NH52).

This gene encodes a membrane protein associated with the Golgi apparatus, which plays a crucial role in intracellular vesicular transport. The encoded protein is likely associated with the late (trans) Golgi compartments, which are involved in the delivery of secretory and membrane proteins to the endosome, lysosome or the plasma membrane. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 780776 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_001079512

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20398
Approved symbol	TVP23A
Name	trans-golgi network vesicle protein 23 homolog A
Location	16p13.13
Locus type	gene with protein product
Status	Approved
Aliases	YDR084C
Ensembl gene	ENSG00000166676
Ensembl biotype	protein_coding
Entrez	780776

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 8 protein_coding, 4 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000299866, ENST00000456096, ENST00000570692, ENST00000572102, ENST00000572428, ENST00000572980, ENST00000573360, ENST00000573857, ENST00000575135, ENST00000619408, ENST00000649981, ENST00000851306, ENST00000922304, ENST00000922305, ENST00000922306

RefSeq mRNA: 2 — MANE Select: NM_001079512 NM_001079512, NM_001318873

CCDS: CCDS45408

Canonical transcript exons

ENST00000299866 — 8 exons

Exon	Start	End
ENSE00001490040	10818485	10818794
ENSE00003467681	10774952	10775096
ENSE00003487700	10771670	10771798
ENSE00003542877	10773313	10773441
ENSE00003596152	10818103	10818182
ENSE00003636888	10774039	10774128
ENSE00003789921	10770272	10770331
ENSE00003849684	10766675	10769101

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 84.21.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4707 / max 80.9913, expressed in 328 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156220	0.6766	244
156222	0.5003	199
156223	0.1735	81
156217	0.0683	19
156221	0.0222	7
156216	0.0163	6
156218	0.0135	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	84.21	gold quality
cortical plate	UBERON:0005343	83.04	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.63	gold quality
endothelial cell	CL:0000115	80.00	gold quality
ventricular zone	UBERON:0003053	79.01	gold quality
anterior cingulate cortex	UBERON:0009835	78.88	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.79	gold quality
ganglionic eminence	UBERON:0004023	78.50	gold quality
right frontal lobe	UBERON:0002810	78.22	gold quality
prefrontal cortex	UBERON:0000451	78.17	gold quality
left ovary	UBERON:0002119	77.80	gold quality
Brodmann (1909) area 9	UBERON:0013540	76.80	gold quality
germinal epithelium of ovary	UBERON:0001304	76.53	silver quality
hypothalamus	UBERON:0001898	76.47	gold quality
right ovary	UBERON:0002118	75.84	gold quality
ovary	UBERON:0000992	75.48	gold quality
neocortex	UBERON:0001950	75.37	gold quality
nucleus accumbens	UBERON:0001882	75.07	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	75.05	gold quality
primary visual cortex	UBERON:0002436	74.38	gold quality
frontal cortex	UBERON:0001870	74.32	gold quality
frontal lobe	UBERON:0016525	74.32	gold quality
caudate nucleus	UBERON:0001873	73.68	gold quality
amygdala	UBERON:0001876	73.66	gold quality
cerebral cortex	UBERON:0000956	72.80	gold quality
putamen	UBERON:0001874	72.05	gold quality
adenohypophysis	UBERON:0002196	71.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.91	gold quality
forebrain	UBERON:0001890	71.67	gold quality
cerebellar hemisphere	UBERON:0002245	71.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

120 targeting TVP23A, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548J-3P	99.94	72.61	4881
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

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tvp23a	ENSMUSG00000050908
rattus_norvegicus	Tvp23a	ENSRNOG00000079813
drosophila_melanogaster	CG5021	FBGN0035944
caenorhabditis_elegans		WBGENE00016400

Paralogs (2): TVP23B (ENSG00000171928), TVP23C (ENSG00000175106)

Protein

Protein identifiers

Golgi apparatus membrane protein TVP23 homolog A — A6NH52 (reviewed: A6NH52)

All UniProt accessions (5): A0A087WYU4, A6NH52, I3L109, I3L3Y3, I3L488

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the TVP23 family.

Isoforms (2)

UniProt ID	Names	Canonical?
A6NH52-1	1	yes
A6NH52-2	2

RefSeq proteins (2): NP_001072980, NP_001305802 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008564	TVP23-like	Family

Pfam: PF05832

UniProt features (6 total): transmembrane region 4, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NH52-F1	79.84	0.47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_SECRETION, MIKKELSEN_ES_ICP_WITH_H3K4ME3, DURAND_STROMA_S_UP, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP, ZNF597_TARGET_GENES, MIR153_5P, MIR616_5P, MIR371B_5P, MIR373_5P, MIR6867_5P, MIR7856_5P, MIR4533, MIR4760_3P, MIR6876_5P

GO Biological Process (2): protein secretion (GO:0009306), vesicle-mediated transport (GO:0016192)

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

GO Cellular Component (2): Golgi membrane (GO:0000139), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein transport	1
secretion by cell	1
establishment of protein localization to extracellular region	1
protein localization to extracellular region	1
transport	1
cellular process	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

290 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TVP23A	FAM24A	A6NFZ4	507
TVP23A	OR10H4	Q8NGA5	507
TVP23A	EPHX4	Q8IUS5	489
TVP23A	NEXMIF	Q5QGS0	478
TVP23A	COP1	Q8NHY2	465
TVP23A	FBXL17	Q9UF56	456
TVP23A	GSC	P56915	451
TVP23A	CACNA1I	Q9P0X4	440
TVP23A	ZSCAN21	Q9Y5A6	430
TVP23A	PLA2G4F	Q68DD2	429
TVP23A	LANCL3	Q6ZV70	371
TVP23A	SLC25A39	Q9BZJ4	359
TVP23A	FBXL13	Q8NEE6	327
TVP23A	SIRAL2	Q9NWS6	325
TVP23A	TENM1	Q9UKZ4	318

IntAct

11 interactions, top by confidence:

A	B	Type	Score
TVP23A	SCAND1	psi-mi:“MI:0915”(physical association)	0.560
TVP23A	WIPF2	psi-mi:“MI:0915”(physical association)	0.560
TVP23A	LEPROTL1	psi-mi:“MI:0915”(physical association)	0.560
TVP23A	YIPF1	psi-mi:“MI:0915”(physical association)	0.400
WIPF2	TVP23A	psi-mi:“MI:0915”(physical association)	0.000
SCAND1	TVP23A	psi-mi:“MI:0915”(physical association)	0.000
TVP23A	LEPROTL1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): TVP23A (Synthetic Lethality), TVP23A (Affinity Capture-RNA), TVP23A (Two-hybrid), SCAND1 (Two-hybrid), WIPF2 (Two-hybrid), YIPF1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVZ9, A4IFN5, A5PK40, A6NH52, A6NI61, B2LYG4, B2RZC9, B6ID01, D2HKB0, D3ZG27, P86229, Q0VDI3, Q15012, Q15546, Q17QJ2, Q1RLT2, Q2TA01, Q4R4I5, Q4R6E8, Q5H8A4, Q5R7Q1, Q5RAH0, Q5RL79, Q5U3C3, Q5VTY9, Q5ZML7, Q64232, Q6PHN7, Q6QRN8, Q719N3, Q71SV0, Q8BWB6, Q8IY49, Q8N6M3, Q8NFT2, Q8R189, Q8VD53, Q8VDI9, Q8VDR5, Q9CQC4

Diamond homologs: A1CIM7, A1CW41, A2Q9P5, A3LRT4, A4RME3, A5DRE8, A6NH52, A6SFL7, A6ZY50, A7TGB4, A8N1Z1, B0CQN9, B0Y4Q8, B2ALT5, P38962, Q0CSZ7, Q0UV43, Q18449, Q1E9X9, Q29S14, Q2UUK2, Q4WQJ5, Q54LC9, Q5APA2, Q5R9I4, Q6BVH1, Q6C7V5, Q6CTK9, Q6FM91, Q74ZP5, Q7SGB6, Q8IQC1, Q8LEK2, Q96ET8, Q9D8T4, Q9NYZ1, Q9Y7K7, Q86I95, Q8N769

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2736 predictions. Top by Δscore:

Variant	Effect	Δscore
16:10761359:CGTA:C	acceptor_loss	1.0000
16:10761360:GTAG:G	acceptor_loss	1.0000
16:10761361:TA:T	acceptor_loss	1.0000
16:10761362:A:AG	acceptor_gain	1.0000
16:10761362:A:AT	acceptor_loss	1.0000
16:10761362:AGGAG:A	acceptor_gain	1.0000
16:10761363:G:GG	acceptor_gain	1.0000
16:10761363:GGA:G	acceptor_gain	1.0000
16:10761363:GGAGG:G	acceptor_gain	1.0000
16:10761472:AAG:A	donor_loss	1.0000
16:10761474:GGTG:G	donor_loss	1.0000
16:10761475:G:T	donor_loss	1.0000
16:10763761:CAT:C	acceptor_gain	1.0000
16:10763763:TC:T	acceptor_loss	1.0000
16:10763764:C:CC	acceptor_gain	1.0000
16:10763765:T:C	acceptor_loss	1.0000
16:10771669:CCGT:C	donor_gain	1.0000
16:10773442:C:CA	acceptor_loss	1.0000
16:10773443:T:C	acceptor_loss	1.0000
16:10774041:T:A	donor_gain	1.0000
16:10774124:ACATT:A	acceptor_gain	1.0000
16:10774125:CATT:C	acceptor_gain	1.0000
16:10774125:CATTC:C	acceptor_gain	1.0000
16:10774127:TT:T	acceptor_gain	1.0000
16:10774129:C:CC	acceptor_gain	1.0000
16:10818116:T:A	donor_gain	1.0000
16:10761354:A:AG	acceptor_gain	0.9900
16:10761359:C:CA	acceptor_gain	0.9900
16:10761362:AG:A	acceptor_gain	0.9900
16:10761363:GG:G	acceptor_gain	0.9900

AlphaMissense

1412 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:10774952:C:A	K78N	0.997
16:10774952:C:G	K78N	0.997
16:10773363:A:G	W135R	0.995
16:10773363:A:T	W135R	0.995
16:10774095:A:G	W90R	0.995
16:10774095:A:T	W90R	0.995
16:10774118:C:T	G82E	0.995
16:10773394:G:C	F124L	0.994
16:10773394:G:T	F124L	0.994
16:10773396:A:G	F124L	0.994
16:10774126:A:C	N79K	0.993
16:10774126:A:T	N79K	0.993
16:10774964:G:C	F74L	0.993
16:10774964:G:T	F74L	0.993
16:10774966:A:G	F74L	0.993
16:10774100:A:G	L88P	0.992
16:10774968:T:A	D73V	0.992
16:10775052:G:T	A45D	0.992
16:10771752:C:T	G167D	0.991
16:10771760:G:C	N164K	0.991
16:10771760:G:T	N164K	0.991
16:10774118:C:A	G82V	0.991
16:10774119:C:G	G82R	0.991
16:10774119:C:T	G82R	0.991
16:10774051:A:C	F104L	0.990
16:10774051:A:T	F104L	0.990
16:10774053:A:G	F104L	0.990
16:10775054:A:C	S44R	0.990
16:10775054:A:T	S44R	0.990
16:10775056:T:G	S44R	0.990

dbSNP variants (sampled 300 via entrez): RS1000001403 (16:10817706 G>A), RS1000004819 (16:10784702 C>T), RS1000007251 (16:10809774 C>T), RS1000036157 (16:10795326 C>T), RS1000043470 (16:10762721 A>G), RS1000161348 (16:10815010 C>T), RS1000186172 (16:10756971 T>C), RS1000237357 (16:10781572 C>G), RS1000245063 (16:10804873 A>T), RS1000317748 (16:10782679 T>A), RS1000350360 (16:10810301 C>A), RS1000428908 (16:10771636 G>A), RS1000456266 (16:10792285 C>T), RS1000498411 (16:10759843 C>G,T), RS1000505338 (16:10791516 C>A)

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
GCST009391_1121	Metabolite levels	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010523	phosphoglyceric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases methylation	6
trichostatin A	affects cotreatment, decreases expression	3
bisphenol A	decreases expression, decreases methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
sulforaphane	increases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Panobinostat	affects cotreatment, decreases expression	1
Urethane	decreases expression	1
Cadmium Chloride	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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