VIT

Summary

VIT (vitrin, HGNC:12697) is a protein-coding gene on chromosome 2p22.2, encoding Vitrin (Q6UXI7). Promotes matrix assembly and cell adhesiveness.

This gene encodes an extracellular matrix (ECM) protein. The protein may be associated with cell adhesion and migration. High levels of expression of the protein in specific parts of the brain suggest its likely role in neural development.

Source: NCBI Gene 5212 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 164 total
• MANE Select transcript: NM_053276

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12697
Approved symbol	VIT
Name	vitrin
Location	2p22.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205221
Ensembl biotype	protein_coding
OMIM	617693
Entrez	5212

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 9 protein_coding

ENST00000379241, ENST00000379242, ENST00000389975, ENST00000401530, ENST00000404084, ENST00000457137, ENST00000464309, ENST00000497382, ENST00000960447

RefSeq mRNA: 11 — MANE Select: NM_053276 NM_001177969, NM_001177970, NM_001177971, NM_001177972, NM_001328661, NM_001391966, NM_001391967, NM_001391968, NM_001391969, NM_001391970, NM_053276

CCDS: CCDS33180, CCDS54347, CCDS54348, CCDS54349, CCDS54350

Canonical transcript exons

ENST00000379242 — 16 exons

Exon	Start	End
ENSE00001480224	36808472	36808985
ENSE00001480225	36805438	36805664
ENSE00001480226	36801301	36801404
ENSE00001480230	36781727	36781771
ENSE00003459795	36773791	36773847
ENSE00003549907	36716353	36716422
ENSE00003566689	36729426	36729491
ENSE00003597949	36767094	36767285
ENSE00003599970	36783340	36783402
ENSE00003626409	36787129	36787276
ENSE00003645265	36743100	36743256
ENSE00003665251	36758969	36759046
ENSE00003669488	36754921	36755054
ENSE00003693840	36775002	36775067
ENSE00003923617	36814183	36814794
ENSE00003930633	36696707	36696973

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 96.45.

FANTOM5 (CAGE): breadth broad, TPM avg 3.8683 / max 292.1633, expressed in 522 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
19742	1.6863	391
19744	1.2748	319
19743	0.8790	298
202158	0.0283	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibia	UBERON:0000979	96.45	gold quality
tibial nerve	UBERON:0001323	95.27	gold quality
mucosa of stomach	UBERON:0001199	92.60	gold quality
tibialis anterior	UBERON:0001385	89.34	silver quality
calcaneal tendon	UBERON:0003701	88.88	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.85	gold quality
pancreatic ductal cell	CL:0002079	88.21	silver quality
sural nerve	UBERON:0015488	87.25	gold quality
left ventricle myocardium	UBERON:0006566	86.92	silver quality
apex of heart	UBERON:0002098	86.60	gold quality
synovial joint	UBERON:0002217	86.59	gold quality
left ovary	UBERON:0002119	85.93	gold quality
left coronary artery	UBERON:0001626	85.66	gold quality
right coronary artery	UBERON:0001625	85.23	gold quality
right atrium auricular region	UBERON:0006631	85.22	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.14	gold quality
layer of synovial tissue	UBERON:0007616	85.08	gold quality
coronary artery	UBERON:0001621	84.89	gold quality
cardiac atrium	UBERON:0002081	84.80	gold quality
right ovary	UBERON:0002118	84.36	gold quality
lower esophagus muscularis layer	UBERON:0035833	83.73	gold quality
lower esophagus	UBERON:0013473	83.60	gold quality
tibial artery	UBERON:0007610	83.47	gold quality
popliteal artery	UBERON:0002250	83.46	gold quality
deltoid	UBERON:0001476	83.12	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.99	gold quality
adipose tissue	UBERON:0001013	82.90	gold quality
heart left ventricle	UBERON:0002084	82.80	gold quality
gastrocnemius	UBERON:0001388	82.55	gold quality
muscle of leg	UBERON:0001383	82.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	37.36

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AHR

miRNA regulators (miRDB)

19 targeting VIT, 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-548C-3P	99.99	74.01	7587
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-6507-5P	99.36	70.46	2524
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-6796-3P	98.68	65.49	689
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-3189-5P	97.55	66.71	655
HSA-MIR-4764-3P	96.81	67.94	580

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	vit	ENSDARG00000063631
mus_musculus	Vit	ENSMUSG00000024076
rattus_norvegicus	Vit	ENSRNOG00000004706

Paralogs (12): COCH (ENSG00000100473), COL12A1 (ENSG00000111799), MATN4 (ENSG00000124159), MATN3 (ENSG00000132031), MATN2 (ENSG00000132561), MATN1 (ENSG00000162510), COL6A3 (ENSG00000163359), VWA2 (ENSG00000165816), COL6A5 (ENSG00000172752), VWA1 (ENSG00000179403), COL14A1 (ENSG00000187955), COL6A6 (ENSG00000206384)

Protein

Protein identifiers

Vitrin — Q6UXI7 (reviewed: Q6UXI7)

All UniProt accessions (4): Q6UXI7, B5MD45, C9J6F5, H7C587

UniProt curated annotations — full annotation on UniProt →

Function. Promotes matrix assembly and cell adhesiveness. Plays a role in spinal cord formation by regulating the proliferation and differentiation of neural stem cells.

Subunit / interactions. Binds dermatan sulfate and chondroitin sulfate.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Isoforms (5)

UniProt ID	Names	Canonical?
Q6UXI7-1	1	yes
Q6UXI7-2	2
Q6UXI7-3	3
Q6UXI7-4	4
Q6UXI7-5	5

RefSeq proteins (11): NP_001171440, NP_001171441, NP_001171442, NP_001171443, NP_001315590, NP_001378895, NP_001378896, NP_001378897, NP_001378898, NP_001378899, NP_444506* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002035	VWF_A	Domain
IPR004043	LCCL	Domain
IPR036465	vWFA_dom_sf	Homologous_superfamily
IPR036609	LCCL_sf	Homologous_superfamily
IPR050525	ECM_Assembly_Org	Family

Pfam: PF00092, PF03815

UniProt features (27 total): splice variant 5, sequence conflict 5, sequence variant 3, domain 3, compositionally biased region 3, glycosylation site 2, disulfide bond 2, region of interest 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXI7-F1	77.13	0.52

Functional residue map

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

Disulfide bonds (2): 46–62, 66–86

Glycosylation sites (2): 390, 520

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 101 (showing top): GOBP_SPINAL_CORD_DEVELOPMENT, FREAC2_01, MODULE_255, MODULE_317, FOXO4_01, EFC_Q6, CEBPB_01, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, TCF4_Q5, IRF7_01, AP1_Q4_01, GATA6_01, WTGAAAT_UNKNOWN, TGANTCA_AP1_C, HFH1_01

GO Biological Process (4): positive regulation of cell-substrate adhesion (GO:0010811), spinal cord development (GO:0021510), extracellular matrix organization (GO:0030198), nervous system development (GO:0007399)

GO Molecular Function (1): glycosaminoglycan binding (GO:0005539)

GO Cellular Component (3): interstitial matrix (GO:0005614), extracellular region (GO:0005576), extracellular matrix (GO:0031012)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of cell-substrate adhesion	1
cell-substrate adhesion	1
positive regulation of cell adhesion	1
central nervous system development	1
anatomical structure development	1
extracellular structure organization	1
external encapsulating structure organization	1
system development	1
carbohydrate derivative binding	1
extracellular matrix	1
cellular anatomical structure	1
external encapsulating structure	1

Protein interactions and networks

STRING

994 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VIT	KCNG3	Q8TAE7	382
VIT	HECTD3	Q5T447	367
VIT	FAM180B	Q6P0A1	366
VIT	ACER2	Q5QJU3	355
VIT	SRM	P19623	353
VIT	CCKAR	P32238	349
VIT	FAM20C	Q8IXL6	349
VIT	NOSIP	Q9Y314	349
VIT	EPYC	Q99645	342
VIT	MAP1LC3C	Q9BXW4	339
VIT	MYOC	Q99972	328
VIT	CHAD	O15335	323
VIT	TSPYL6	Q8N831	322
VIT	OPTC	Q9UBM4	319
VIT	HRCT1	Q6UXD1	313

IntAct

3 interactions, top by confidence:

A	B	Type	Score
VIT	COCH	psi-mi:“MI:0914”(association)	0.530

BioGRID (5): HSPA5 (Affinity Capture-MS), COCH (Affinity Capture-MS), COCH (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), ACTR1B (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A4FUF0, A5YT95, O35276, O35375, O42163, O43405, O60462, O62650, P07224, P07225, P10669, P18614, P19883, P21674, P26012, P26013, P31514, P31515, P47931, P50291, P56199, P84552, P98118, Q07257, Q0VBD0, Q15223, Q28520, Q3V3R4, Q49A26, Q562D5, Q5EA64, Q5R7T2, Q5RKH0, Q5ZLS7, Q62507, Q62935, Q6IS24, Q6UXI7, Q6ZQ11, Q7TT15

Diamond homologs: A0A1D5NSM8, A0JNA2, A2AVA0, A2AX52, D3YXF5, O02839, O19063, O35764, O43405, O70340, O76536, O89029, O95502, O96530, P02741, P02743, P06205, P06206, P06207, P06681, P07202, P07629, P08607, P09871, P0C6B8, P10643, P12246, P13944, P14151, P14847, P15697, P18337, P23680, P32018, P47970, P47971, P47972, P48199, P49254, P49262

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	142
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2695 predictions. Top by Δscore:

Variant	Effect	Δscore
2:36716351:AG:A	acceptor_gain	1.0000
2:36716352:GG:G	acceptor_gain	1.0000
2:36729424:A:AG	acceptor_gain	1.0000
2:36729425:G:GG	acceptor_gain	1.0000
2:36729487:GTTCA:G	donor_gain	1.0000
2:36729492:G:GG	donor_gain	1.0000
2:36743098:A:AG	acceptor_gain	1.0000
2:36743098:A:G	acceptor_loss	1.0000
2:36743098:AGCT:A	acceptor_gain	1.0000
2:36743099:G:GA	acceptor_gain	1.0000
2:36743099:GC:G	acceptor_gain	1.0000
2:36743099:GCT:G	acceptor_gain	1.0000
2:36743099:GCTG:G	acceptor_gain	1.0000
2:36743099:GCTGT:G	acceptor_gain	1.0000
2:36743255:AGGT:A	donor_loss	1.0000
2:36743256:GGT:G	donor_loss	1.0000
2:36743258:T:A	donor_loss	1.0000
2:36787160:T:TA	acceptor_gain	1.0000
2:36787161:G:A	acceptor_gain	1.0000
2:36787273:ATGGG:A	donor_loss	1.0000
2:36787274:TGGGT:T	donor_loss	1.0000
2:36787275:GG:G	donor_gain	1.0000
2:36787276:GG:G	donor_gain	1.0000
2:36787276:GGT:G	donor_loss	1.0000
2:36787277:G:GG	donor_gain	1.0000
2:36787277:GTA:G	donor_loss	1.0000
2:36787278:TAAGT:T	donor_loss	1.0000
2:36805631:GCA:G	donor_gain	1.0000
2:36805634:G:GG	donor_gain	1.0000
2:36808468:CTAG:C	acceptor_loss	1.0000

AlphaMissense

4521 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:36808623:T:A	V499D	0.999
2:36808629:A:T	D501V	0.999
2:36808730:G:T	G535W	0.999
2:36808857:C:A	A577D	0.999
2:36808620:T:C	F498S	0.998
2:36808628:G:C	D501H	0.998
2:36808634:T:C	S503P	0.998
2:36808635:C:T	S503F	0.998
2:36808640:A:C	S505R	0.998
2:36808642:T:A	S505R	0.998
2:36808642:T:G	S505R	0.998
2:36808658:T:C	F511L	0.998
2:36808659:T:G	F511C	0.998
2:36808660:C:A	F511L	0.998
2:36808660:C:G	F511L	0.998
2:36808725:G:C	R533P	0.998
2:36808731:G:A	G535E	0.998
2:36808742:T:G	Y539D	0.998
2:36808856:G:C	A577P	0.998
2:36808934:G:T	G603W	0.998
2:36814204:G:A	G627D	0.998
2:36814285:T:G	F654C	0.998
2:36814329:T:A	C669S	0.998
2:36814330:G:A	C669Y	0.998
2:36814330:G:C	C669S	0.998
2:36814331:T:G	C669W	0.998
2:36808616:G:C	G497R	0.997
2:36808617:G:A	G497D	0.997
2:36808626:T:A	I500N	0.997
2:36808629:A:C	D501A	0.997

dbSNP variants (sampled 300 via entrez): RS1000046152 (2:36743382 T>A), RS1000058029 (2:36810107 C>A), RS1000064014 (2:36777352 T>C), RS1000076644 (2:36798743 A>G), RS1000077550 (2:36782884 T>A), RS1000109329 (2:36712259 A>G), RS1000112168 (2:36814405 G>A,C), RS1000117412 (2:36770285 G>A,C,T), RS1000131942 (2:36708957 G>A), RS1000144258 (2:36793003 C>T), RS1000154415 (2:36783113 G>C), RS1000160672 (2:36721974 T>C), RS1000192906 (2:36701913 C>T), RS1000198236 (2:36772736 A>T), RS1000199101 (2:36699443 T>C)

Disease associations

OMIM: gene MIM:617693 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST003901_16	Cognitive decline (age-related)	5.000000e-06
GCST004639_22	Prudent dietary pattern	4.000000e-06
GCST006585_740	Blood protein levels	1.000000e-20
GCST006585_942	Blood protein levels	1.000000e-26
GCST010697_37	Cortical surface area (min-P)	6.000000e-31
GCST010698_20	Subcortical volume (min-P)	1.000000e-08
GCST010699_106	Brain morphology (min-P)	2.000000e-11
GCST010700_34	Cortical thickness (MOSTest)	2.000000e-08
GCST010701_57	Cortical surface area (MOSTest)	4.000000e-16
GCST010702_109	Subcortical volume (MOSTest)	1.000000e-09
GCST010703_96	Brain morphology (MOSTest)	6.000000e-46

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	3
Arsenic Trioxide	decreases expression	2
Dexamethasone	increases expression, affects cotreatment	2
Silicon Dioxide	decreases expression, increases expression	2
bisphenol A	affects cotreatment, increases expression	1
trichostatin A	increases expression	1
sulforaphane	decreases expression	1
sodium arsenite	decreases expression	1
aflatoxin B2	decreases methylation	1
nickel sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression	1
incobotulinumtoxinA	increases expression	1
Cadmium	decreases expression	1
Cisplatin	increases response to substance	1
Diethylhexyl Phthalate	increases expression	1
Doxorubicin	increases response to substance	1
Indomethacin	affects cotreatment, increases expression	1
Methotrexate	increases response to substance	1
Nickel	decreases expression	1
Valproic Acid	increases expression	1
Vincristine	increases response to substance	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	increases methylation	1
Paclitaxel	increases response to substance	1
Topotecan	increases response to substance	1

Clinical trials (associated diseases)

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