VRTN

Summary

VRTN (vertebrae development associated, HGNC:20223) is a protein-coding gene on chromosome 14q24.3, encoding Vertnin (Q9H8Y1). Acts as a transcription factor that regulates development of thoracic vertebrae.

Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be active in chromatin.

Source: NCBI Gene 55237 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 113 total
• MANE Select transcript: NM_018228

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20223
Approved symbol	VRTN
Name	vertebrae development associated
Location	14q24.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10811, vertnin
Ensembl gene	ENSG00000133980
Ensembl biotype	protein_coding
OMIM	620468
Entrez	55237

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000256362, ENST00000557177, ENST00000925859, ENST00000925860, ENST00000925861, ENST00000925862, ENST00000925863, ENST00000925864, ENST00000925865, ENST00000925866, ENST00000925867, ENST00000925868

RefSeq mRNA: 1 — MANE Select: NM_018228 NM_018228

CCDS: CCDS9830

Canonical transcript exons

ENST00000256362 — 2 exons

Exon	Start	End
ENSE00000911935	74356783	74360008
ENSE00001236472	74348471	74348652

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 89.82.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 3.4208 / max 191.4981, expressed in 131 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
140572	2.9029	130
140573	0.5179	83

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	89.82	gold quality
vena cava	UBERON:0004087	88.10	silver quality
cerebellar vermis	UBERON:0004720	84.64	gold quality
gluteal muscle	UBERON:0002000	84.13	gold quality
triceps brachii	UBERON:0001509	83.95	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	83.31	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	82.62	gold quality
diaphragm	UBERON:0001103	82.31	gold quality
inferior olivary complex	UBERON:0002127	81.90	gold quality
tongue squamous epithelium	UBERON:0006919	81.68	gold quality
tendon of biceps brachii	UBERON:0008188	80.99	gold quality
pons	UBERON:0000988	79.78	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.92	gold quality
pharyngeal mucosa	UBERON:0000355	78.70	gold quality
pylorus	UBERON:0001166	78.70	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	78.64	gold quality
lateral nuclear group of thalamus	UBERON:0002736	78.53	gold quality
pericardium	UBERON:0002407	78.43	silver quality
oocyte	CL:0000023	78.37	silver quality
vastus lateralis	UBERON:0001379	78.37	gold quality
olfactory bulb	UBERON:0002264	77.83	gold quality
sperm	CL:0000019	77.72	gold quality
male germ cell	CL:0000015	77.65	gold quality
cardia of stomach	UBERON:0001162	77.52	silver quality
biceps brachii	UBERON:0001507	77.50	gold quality
quadriceps femoris	UBERON:0001377	77.35	gold quality
substantia nigra pars compacta	UBERON:0001965	77.19	gold quality
type B pancreatic cell	CL:0000169	77.15	gold quality
heart right ventricle	UBERON:0002080	76.40	gold quality
lateral globus pallidus	UBERON:0002476	76.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-10018	yes	106.60
E-MTAB-3929	yes	92.55
E-MTAB-9388	yes	12.20
E-CURD-10	no	2.69
E-ANND-3	no	2.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting VRTN, 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-9-5P	100.00	72.28	2361
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6755-5P	99.95	65.59	464
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-4263	99.18	69.25	2236
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-12125	98.59	67.54	1044
HSA-MIR-1304-3P	98.29	66.44	1207
HSA-MIR-6867-3P	98.12	66.07	1305
HSA-MIR-7112-3P	97.67	68.77	948
HSA-MIR-6793-3P	97.66	65.78	1084
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-6508-3P	96.73	65.48	576
HSA-MIR-5009-5P	94.82	63.89	775
HSA-MIR-8058	94.76	63.41	632

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	vrtn	ENSDARG00000061963
mus_musculus	Vrtn	ENSMUSG00000071235
rattus_norvegicus	Vrtn	ENSRNOG00000048378

Protein

Protein identifiers

Vertnin — Q9H8Y1 (reviewed: Q9H8Y1)

All UniProt accessions (2): Q9H8Y1, G3V537

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcription factor that regulates development of thoracic vertebrae.

Subcellular location. Nucleus.

Similarity. Belongs to the vertnin family.

RefSeq proteins (1): NP_060698* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010921	Trp_repressor/repl_initiator	Homologous_superfamily
IPR038822	Vertnin-like	Family
IPR047273	VRTN_OTU_dom	Domain

UniProt features (6 total): sequence variant 2, chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H8Y1-F1	70.66	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): chr14q24, SHEN_SMARCA2_TARGETS_DN, BENPORATH_ES_1, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MODULE_495, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, MIKKELSEN_IPS_ICP_WITH_H3K27ME3, MIKKELSEN_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3, ATF2_UP.V1_UP, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_UP, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_DN, H1_6_TARGET_GENES, SNIP1_TARGET_GENES, ZNF597_TARGET_GENES, ZNF8_TARGET_GENES

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (3): sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA binding	1
nucleic acid binding	1
binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

562 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VRTN	PROX2	Q3B8N5	726
VRTN	SYNDIG1L	A6NDD5	704
VRTN	ABCD4	O14678	651
VRTN	AREL1	O15033	622
VRTN	NR6A1	Q15406	615
VRTN	ANKRD46	Q86W74	484
VRTN	DNAAF10	Q96MX6	477
VRTN	LRRC74A	Q0VAA2	470
VRTN	TMEM192	Q8IY95	469
VRTN	LTBP2	Q14767	455
VRTN	OR10R2	Q8NGX6	447
VRTN	SYBU	Q9NX95	444
VRTN	PDIA4	P13667	443
VRTN	FAM161B	Q96MY7	434
VRTN	YLPM1	P49750	430

IntAct

41 interactions, top by confidence:

A	B	Type	Score
C9orf72	VRTN	psi-mi:“MI:0915”(physical association)	0.600
VRTN	C9orf72	psi-mi:“MI:0915”(physical association)	0.600
POLR3C	VRTN	psi-mi:“MI:0915”(physical association)	0.560
RAB3D	VRTN	psi-mi:“MI:0915”(physical association)	0.560
RAB2B	VRTN	psi-mi:“MI:0915”(physical association)	0.560
CTBP2	VRTN	psi-mi:“MI:0915”(physical association)	0.560
RAB3A	VRTN	psi-mi:“MI:0915”(physical association)	0.560
EIF4A3	VRTN	psi-mi:“MI:0915”(physical association)	0.560
RAB3B	VRTN	psi-mi:“MI:0915”(physical association)	0.560
FAM90A1	VRTN	psi-mi:“MI:0915”(physical association)	0.560
RAB3C	VRTN	psi-mi:“MI:0915”(physical association)	0.560
VRTN	CCT6B	psi-mi:“MI:0914”(association)	0.350
RAB2B	VRTN	psi-mi:“MI:0915”(physical association)	0.000
C9orf72	VRTN	psi-mi:“MI:0915”(physical association)	0.000
CTBP2	VRTN	psi-mi:“MI:0915”(physical association)	0.000
RAB3A	VRTN	psi-mi:“MI:0915”(physical association)	0.000
EIF4A3	VRTN	psi-mi:“MI:0915”(physical association)	0.000
FAM90A1	VRTN	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): VRTN (Affinity Capture-MS), VRTN (Two-hybrid), VRTN (Two-hybrid), VRTN (Two-hybrid), EIF4A3 (Two-hybrid), C9orf72 (Two-hybrid), RAB3C (Two-hybrid), RAB3B (Two-hybrid), FAM90A1 (Two-hybrid), CTBP2 (Two-hybrid), POLR3C (Two-hybrid), VRTN (Affinity Capture-MS), CCT6B (Affinity Capture-MS), ZHX2 (Affinity Capture-MS), SALL1 (Affinity Capture-MS)

ESM2 similar proteins: A4Q9E5, A4Q9F1, A6PVC2, B1H224, D2GZW6, E1BP92, E1CHH8, E9PT87, O15037, O43918, O94966, O95238, P27987, P29473, P42335, P48778, P59729, Q1ECV4, Q2TAK8, Q3SYK4, Q3UIZ8, Q3UJD6, Q4R739, Q5JYT7, Q6B0I6, Q6DID5, Q6J1Y9, Q6NZK8, Q75NR7, Q7TSI1, Q80U38, Q810F8, Q8BV79, Q8BWG4, Q8CHB8, Q8N841, Q8NC06, Q8NE63, Q8TB24, Q8VDG6

Diamond homologs: D2GZW6, E1BP92, E1CHH8, Q08C99, Q3SYK4, Q9H8Y1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	105
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

96 predictions. Top by Δscore:

Variant	Effect	Δscore
14:74356772:T:TA	acceptor_gain	1.0000
14:74356777:T:TA	acceptor_gain	1.0000
14:74356778:GGCA:G	acceptor_loss	1.0000
14:74356780:CAGG:C	acceptor_loss	1.0000
14:74356781:A:AG	acceptor_gain	1.0000
14:74356781:AG:A	acceptor_gain	1.0000
14:74356781:AGGA:A	acceptor_loss	1.0000
14:74356781:AGGAT:A	acceptor_gain	1.0000
14:74356782:G:GT	acceptor_gain	1.0000
14:74356782:GG:G	acceptor_gain	1.0000
14:74356782:GGA:G	acceptor_gain	1.0000
14:74356782:GGAT:G	acceptor_gain	1.0000
14:74356782:GGATG:G	acceptor_gain	1.0000
14:74348649:CCAG:C	donor_loss	0.9900
14:74348650:CAGG:C	donor_loss	0.9900
14:74348653:GTC:G	donor_loss	0.9900
14:74348654:T:A	donor_loss	0.9900
14:74356778:G:A	acceptor_gain	0.9800
14:74348653:G:GG	donor_gain	0.9700
14:74348656:A:AG	donor_gain	0.9500
14:74348657:G:GG	donor_gain	0.9500
14:74356767:T:G	acceptor_gain	0.9300
14:74348585:C:G	donor_gain	0.9100
14:74348633:GGCTC:G	donor_gain	0.9000
14:74356766:A:AG	acceptor_gain	0.8600
14:74356777:TGGCA:T	acceptor_gain	0.8600
14:74356778:GGCAG:G	acceptor_gain	0.8600
14:74356779:GCAGG:G	acceptor_gain	0.8600
14:74356780:CAGGA:C	acceptor_gain	0.8500
14:74356781:A:G	acceptor_gain	0.8500

AlphaMissense

4508 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:74357447:T:A	W222R	0.999
14:74357447:T:C	W222R	0.999
14:74357787:T:C	F335S	0.999
14:74357822:T:G	Y347D	0.999
14:74358089:T:G	Y436D	0.999
14:74358098:T:A	W439R	0.999
14:74358098:T:C	W439R	0.999
14:74358848:T:A	W689R	0.999
14:74358848:T:C	W689R	0.999
14:74357303:T:A	W174R	0.998
14:74357303:T:C	W174R	0.998
14:74357449:G:C	W222C	0.998
14:74357449:G:T	W222C	0.998
14:74357831:T:A	W350R	0.998
14:74357831:T:C	W350R	0.998
14:74358054:T:C	F424S	0.998
14:74358100:G:C	W439C	0.998
14:74358100:G:T	W439C	0.998
14:74358102:G:C	R440P	0.998
14:74358759:T:C	L659S	0.998
14:74358804:T:C	F674S	0.998
14:74358850:G:C	W689C	0.998
14:74358850:G:T	W689C	0.998
14:74357786:T:C	F335L	0.997
14:74357788:C:A	F335L	0.997
14:74357788:C:G	F335L	0.997
14:74357798:T:C	F339L	0.997
14:74357800:C:A	F339L	0.997
14:74357800:C:G	F339L	0.997
14:74358065:T:C	F428L	0.997

dbSNP variants (sampled 300 via entrez): RS1000075418 (14:74340282 T>C), RS1000137388 (14:74333790 A>G), RS1000145514 (14:74339087 C>T), RS1000156160 (14:74337356 CA>C), RS1000339529 (14:74327991 G>T), RS1000389083 (14:74303928 G>A,C), RS1000465225 (14:74337571 G>A,C), RS1000519763 (14:74335593 T>A,C), RS1000637802 (14:74344288 C>T), RS1000727812 (14:74329994 C>T), RS1000887182 (14:74311266 C>T), RS1000900272 (14:74323314 T>G), RS1000915872 (14:74355058 C>T), RS1000939153 (14:74311006 C>G), RS1000954433 (14:74358386 A>G)

Disease associations

OMIM: gene MIM:620468 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST007429_120	Lung function (FVC)	1.000000e-18
GCST007432_52	FEV1	3.000000e-14
GCST010002_156	Refractive error	7.000000e-25

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004312	vital capacity
EFO:0004314	forced expiratory volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	increases expression, affects cotreatment	2
Valproic Acid	affects expression, decreases expression	2
pirinixic acid	affects binding, increases activity, increases expression	1
bisphenol A	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Diethylhexyl Phthalate	increases expression	1
Ivermectin	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
Cyclosporine	decreases methylation	1
Aflatoxin B1	increases methylation	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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