TVP23B

Summary

TVP23B (trans-golgi network vesicle protein 23 homolog B, HGNC:20399) is a protein-coding gene on chromosome 17p11.2, encoding Golgi apparatus membrane protein TVP23 homolog B (Q9NYZ1).

Predicted to be involved in protein secretion and vesicle-mediated transport. Predicted to be located in membrane. Predicted to be active in Golgi membrane.

Source: NCBI Gene 51030 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_016078

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20399
Approved symbol	TVP23B
Name	trans-golgi network vesicle protein 23 homolog B
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	CGI-148, YDR084C
Ensembl gene	ENSG00000171928
Ensembl biotype	protein_coding
Entrez	51030

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000307767, ENST00000476139, ENST00000482741, ENST00000571018, ENST00000572845, ENST00000574226, ENST00000574294, ENST00000575261, ENST00000581733, ENST00000582288, ENST00000880247, ENST00000880248, ENST00000920914

RefSeq mRNA: 7 — MANE Select: NM_016078 NM_001316919, NM_001316920, NM_001316921, NM_001316922, NM_001316923, NM_001316924, NM_016078

CCDS: CCDS42274, CCDS82084

Canonical transcript exons

ENST00000307767 — 7 exons

Exon	Start	End
ENSE00002649249	18781183	18781305
ENSE00003461775	18797579	18797668
ENSE00003473839	18798812	18798943
ENSE00003476262	18805541	18806714
ENSE00003545095	18790896	18791040
ENSE00003570975	18804138	18804266
ENSE00003659275	18789353	18789435

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 97.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3113 / max 110.5647, expressed in 1510 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159819	2.1266	1098
159820	1.1847	831

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	97.85	gold quality
calcaneal tendon	UBERON:0003701	96.87	gold quality
stromal cell of endometrium	CL:0002255	95.38	gold quality
adrenal tissue	UBERON:0018303	94.43	gold quality
esophagus mucosa	UBERON:0002469	94.41	gold quality
pancreas	UBERON:0001264	94.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.86	gold quality
lower esophagus mucosa	UBERON:0035834	93.75	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.56	gold quality
endometrium	UBERON:0001295	93.54	gold quality
body of pancreas	UBERON:0001150	93.37	gold quality
rectum	UBERON:0001052	93.18	gold quality
adenohypophysis	UBERON:0002196	92.77	gold quality
gall bladder	UBERON:0002110	92.64	gold quality
saliva-secreting gland	UBERON:0001044	92.57	gold quality
minor salivary gland	UBERON:0001830	92.50	gold quality
duodenum	UBERON:0002114	92.28	gold quality
pituitary gland	UBERON:0000007	92.25	gold quality
vagina	UBERON:0000996	92.13	gold quality
adrenal gland	UBERON:0002369	92.09	gold quality
right adrenal gland cortex	UBERON:0035827	92.07	gold quality
left adrenal gland	UBERON:0001234	91.93	gold quality
fallopian tube	UBERON:0003889	91.86	gold quality
tonsil	UBERON:0002372	91.81	gold quality
right adrenal gland	UBERON:0001233	91.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.42	gold quality
thoracic aorta	UBERON:0001515	91.33	gold quality
esophagus	UBERON:0001043	91.29	gold quality
ascending aorta	UBERON:0001496	91.28	gold quality
left adrenal gland cortex	UBERON:0035825	91.28	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)

93 targeting TVP23B, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4282	99.99	75.36	6408
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AQ-3P	99.93	72.66	4867

Literature-anchored findings (GeneRIF, showing 1)

• The role of FAM18B in regulating retinal microvascular endothelial cell viability, migration, and endothelial tube formation was determined following RNAi-mediated knockdown of FAM18B. (PMID:25221423)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:112148	ENSDARG00000001804
danio_rerio	tvp23b	ENSDARG00000057060
mus_musculus	Tvp23b	ENSMUSG00000014177
rattus_norvegicus	AABR07006081.1	ENSRNOG00000016597
rattus_norvegicus	Tvp23b	ENSRNOG00000050649
drosophila_melanogaster	CG5021	FBGN0035944
caenorhabditis_elegans		WBGENE00016400

Paralogs (2): TVP23A (ENSG00000166676), TVP23C (ENSG00000175106)

Protein

Protein identifiers

Golgi apparatus membrane protein TVP23 homolog B — Q9NYZ1 (reviewed: Q9NYZ1)

All UniProt accessions (6): Q9NYZ1, E5RIS5, I3L376, J3KS67, J3QL63, K7ENL4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the TVP23 family.

RefSeq proteins (7): NP_001303848, NP_001303849, NP_001303850, NP_001303851, NP_001303852, NP_001303853, NP_057162* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008564	TVP23-like	Family

Pfam: PF05832

UniProt features (9 total): transmembrane region 4, chain 1, region of interest 1, modified residue 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NYZ1-F1	80.87	0.47

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): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 136 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_SECRETION, MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP, REN_ALVEOLAR_RHABDOMYOSARCOMA_DN, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, LINSLEY_MIR16_TARGETS, DELACROIX_RAR_BOUND_ES, FORTSCHEGGER_PHF8_TARGETS_DN, ERBB2_UP.V1_DN, ALKBH3_TARGET_GENES, ARID5B_TARGET_GENES, CIITA_TARGET_GENES, DIDO1_TARGET_GENES

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

392 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TVP23B	CDRT15	Q96T59	714
TVP23B	TMEM60	Q9H2L4	687
TVP23B	CDRT4	Q8N9R6	658
TVP23B	TEKT3	Q9BXF9	540
TVP23B	TRIM16L	Q309B1	507
TVP23B	TBC1D28	Q2M2D7	506
TVP23B	SMCO2	A6NFE2	448
TVP23B	FBXW10	Q5XX13	447
TVP23B	TMEM87A	Q8NBN3	429
TVP23B	FBXW10B	O95170	418
TVP23B	PIGW	Q7Z7B1	411
TVP23B	TRMT13	Q9NUP7	394
TVP23B	CNIH4	Q9P003	383
TVP23B	HS3ST3B1	Q9Y662	379
TVP23B	MRTFB	Q9ULH7	370

IntAct

80 interactions, top by confidence:

A	B	Type	Score
TVP23B	TMX2	psi-mi:“MI:0915”(physical association)	0.560
TVP23B	SHISA5	psi-mi:“MI:0915”(physical association)	0.560
TVP23B	SLC35C2	psi-mi:“MI:0915”(physical association)	0.560
SYT16	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
PBX3	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
YIPF4	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
CEP19	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
SLC35C2	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
REEP4	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
TMEM80	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
SLC10A6	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
TVP23B	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
SLC10A1	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
TMEM14B	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
TIMMDC1	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
TLCD4	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
YIPF2	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
SCN3B	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
ABHD6	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
SHISA5	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
HSD17B11	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
WLS	TVP23B	psi-mi:“MI:0915”(physical association)	0.490

BioGRID (48): TVP23B (Proximity Label-MS), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid), TVP23B (Two-hybrid)

ESM2 similar proteins: A0A8I3S9V6, A0M8U1, A6NH52, E1BWM5, O35089, P13666, P86050, Q00765, Q0VCK9, Q0X0A5, Q1RLU8, Q29S14, Q2PG42, Q3KNM2, Q3ZC24, Q5BJU5, Q5M7T4, Q5R9I4, Q5R9K4, Q5RE33, Q5T4T1, Q5ZJ41, Q5ZJD7, Q6DD32, Q6GM44, Q6NYF1, Q6P360, Q6PI25, Q7TQ48, Q86TD4, Q8C407, Q8L5Y9, Q8MK44, Q8R1Z9, Q91ZQ0, Q940S0, Q96GC9, Q99K70, Q99KU0, Q9BSR8

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

960 predictions. Top by Δscore:

Variant	Effect	Δscore
17:18781269:G:GT	donor_gain	1.0000
17:18789350:CAG:C	acceptor_loss	1.0000
17:18789351:A:AG	acceptor_gain	1.0000
17:18789351:AG:A	acceptor_gain	1.0000
17:18789352:G:GG	acceptor_gain	1.0000
17:18789352:GG:G	acceptor_gain	1.0000
17:18789352:GGAT:G	acceptor_gain	1.0000
17:18789352:GGATA:G	acceptor_gain	1.0000
17:18789432:TCAG:T	donor_loss	1.0000
17:18789433:CAGG:C	donor_loss	1.0000
17:18789434:AG:A	donor_loss	1.0000
17:18789435:GG:G	donor_loss	1.0000
17:18789436:GTAG:G	donor_loss	1.0000
17:18789437:T:G	donor_loss	1.0000
17:18790886:T:TA	acceptor_gain	1.0000
17:18797577:AGAAT:A	acceptor_gain	1.0000
17:18797578:GA:G	acceptor_gain	1.0000
17:18797578:GAAT:G	acceptor_gain	1.0000
17:18797578:GAATG:G	acceptor_gain	1.0000
17:18797665:AAAGG:A	donor_loss	1.0000
17:18797666:AAGG:A	donor_loss	1.0000
17:18797667:AG:A	donor_loss	1.0000
17:18797668:GGTAA:G	donor_loss	1.0000
17:18797669:G:GA	donor_loss	1.0000
17:18797670:T:A	donor_loss	1.0000
17:18798806:TTATA:T	acceptor_loss	1.0000
17:18798807:TATA:T	acceptor_loss	1.0000
17:18798809:TA:T	acceptor_loss	1.0000
17:18798810:A:G	acceptor_loss	1.0000
17:18798811:GGA:G	acceptor_gain	1.0000

AlphaMissense

1355 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:18791040:G:C	K80N	0.989
17:18791040:G:T	K80N	0.989
17:18798860:T:C	F127L	0.986
17:18798862:T:A	F127L	0.986
17:18798862:T:G	F127L	0.986
17:18797612:T:A	W92R	0.984
17:18797612:T:C	W92R	0.984
17:18797654:T:C	F106L	0.981
17:18797656:T:A	F106L	0.981
17:18797656:T:G	F106L	0.981
17:18791026:T:C	F76L	0.979
17:18791028:T:A	F76L	0.979
17:18791028:T:G	F76L	0.979
17:18791024:A:T	D75V	0.972
17:18797581:T:A	N81K	0.972
17:18797581:T:G	N81K	0.972
17:18798893:T:A	W138R	0.972
17:18798893:T:C	W138R	0.972
17:18790936:A:C	S46R	0.970
17:18790938:T:A	S46R	0.970
17:18790938:T:G	S46R	0.970
17:18791024:A:C	D75A	0.969
17:18797589:G:A	G84D	0.963
17:18804153:G:C	G160R	0.962
17:18791020:T:C	C74R	0.960
17:18791039:A:T	K80M	0.959
17:18791025:C:A	D75E	0.958
17:18791025:C:G	D75E	0.958
17:18797607:T:C	L90P	0.958
17:18797614:G:C	W92C	0.958

dbSNP variants (sampled 300 via entrez): RS1000226487 (17:18801334 G>T), RS1000587913 (17:18788288 G>A), RS1000618941 (17:18788054 T>A,C), RS1000768770 (17:18794287 T>C), RS1001138923 (17:18794720 T>A), RS1001404611 (17:18782485 A>G), RS1001416826 (17:18788944 A>G), RS1001429076 (17:18789149 TC>T), RS1001487527 (17:18781973 G>T), RS1001767274 (17:18782947 A>G), RS1001941231 (17:18793998 AAG>A), RS1001972427 (17:18793756 T>C,G), RS1002323452 (17:18781406 C>T), RS1002354226 (17:18781213 C>G), RS1002465670 (17:18806145 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression, increases expression	3
sodium arsenite	decreases expression, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Cadmium Chloride	increases abundance, increases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
hydroxyhydroquinone	increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	decreases expression	1
bisphenol AF	increases expression	1
Sunitinib	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Oxygen	decreases expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Thiram	increases expression	1
Tretinoin	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Asbestos, Crocidolite	increases expression	1
Copper Sulfate	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Clinical trials (associated diseases)

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