VSIG10

Summary

VSIG10 (V-set and immunoglobulin domain containing 10, HGNC:26078) is a protein-coding gene on chromosome 12q24.23, encoding V-set and immunoglobulin domain-containing protein 10 (Q8N0Z9).

Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion and synapse assembly. Predicted to be located in membrane. Predicted to be active in cell-cell junction and plasma membrane.

Source: NCBI Gene 54621 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 96 total
• MANE Select transcript: NM_019086

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26078
Approved symbol	VSIG10
Name	V-set and immunoglobulin domain containing 10
Location	12q24.23
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000176834
Ensembl biotype	protein_coding
Entrez	54621

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 7 protein_coding_CDS_not_defined, 5 protein_coding, 4 retained_intron

ENST00000321694, ENST00000359236, ENST00000536905, ENST00000538357, ENST00000539956, ENST00000540117, ENST00000541855, ENST00000542011, ENST00000542195, ENST00000545259, ENST00000545722, ENST00000612851, ENST00000621133, ENST00000965105, ENST00000965106, ENST00000965107

RefSeq mRNA: 1 — MANE Select: NM_019086 NM_019086

CCDS: CCDS44992

Canonical transcript exons

ENST00000359236 — 9 exons

Exon	Start	End
ENSE00001293835	118082127	118082429
ENSE00001307615	118071359	118071469
ENSE00001311670	118079346	118079606
ENSE00001326021	118073699	118073992
ENSE00001326828	118068377	118068597
ENSE00001431813	118063593	118066694
ENSE00002245844	118103593	118104011
ENSE00002387355	118071052	118071067
ENSE00003531090	118095533	118095814

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 96.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.6710 / max 213.6533, expressed in 1706 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
133540	2.9573	1155
133543	2.9235	1255
133539	1.2392	739
133544	1.1596	676
133537	0.9486	433
133538	0.4427	241

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	96.88	gold quality
rectum	UBERON:0001052	92.65	gold quality
jejunal mucosa	UBERON:0000399	92.56	gold quality
right adrenal gland cortex	UBERON:0035827	91.04	gold quality
mucosa of transverse colon	UBERON:0004991	90.69	gold quality
pancreatic ductal cell	CL:0002079	90.46	gold quality
right adrenal gland	UBERON:0001233	90.17	gold quality
adrenal cortex	UBERON:0001235	89.93	gold quality
left adrenal gland	UBERON:0001234	89.90	gold quality
left adrenal gland cortex	UBERON:0035825	89.89	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.47	gold quality
right lobe of thyroid gland	UBERON:0001119	89.46	gold quality
transverse colon	UBERON:0001157	89.32	gold quality
small intestine	UBERON:0002108	89.22	gold quality
colonic mucosa	UBERON:0000317	89.08	gold quality
left lobe of thyroid gland	UBERON:0001120	88.67	gold quality
adrenal gland	UBERON:0002369	88.64	gold quality
right lung	UBERON:0002167	88.62	gold quality
thyroid gland	UBERON:0002046	88.49	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.45	gold quality
mucosa of sigmoid colon	UBERON:0004993	88.42	gold quality
lower esophagus mucosa	UBERON:0035834	88.33	gold quality
duodenum	UBERON:0002114	88.30	gold quality
esophagus squamous epithelium	UBERON:0006920	88.03	gold quality
left ovary	UBERON:0002119	87.97	gold quality
right ovary	UBERON:0002118	87.70	gold quality
amniotic fluid	UBERON:0000173	87.68	gold quality
ileal mucosa	UBERON:0000331	87.47	gold quality
body of pancreas	UBERON:0001150	87.26	gold quality
right lobe of liver	UBERON:0001114	87.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	15.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

138 targeting VSIG10, 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-4533	100.00	69.48	2758
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-128-3P	99.95	71.17	2484

Literature-anchored findings (GeneRIF, showing 1)

• Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans. (PMID:36400179)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Vsig10	ENSMUSG00000066894
rattus_norvegicus	Vsig10	ENSRNOG00000022698

Paralogs (36): CNTN1 (ENSG00000018236), CDON (ENSG00000064309), NEO1 (ENSG00000067141), SDK2 (ENSG00000069188), IGSF9B (ENSG00000080854), IGSF9 (ENSG00000085552), NRCAM (ENSG00000091129), MXRA5 (ENSG00000101825), IGDCC4 (ENSG00000103742), CNTN3 (ENSG00000113805), IGSF21 (ENSG00000117154), CNTN6 (ENSG00000134115), CHL1 (ENSG00000134121), PTPRQ (ENSG00000139304), CNTN4 (ENSG00000144619), BOC (ENSG00000144857), SDK1 (ENSG00000146555), HMCN2 (ENSG00000148357), NCAM1 (ENSG00000149294), CNTN5 (ENSG00000149972), IGSF10 (ENSG00000152580), ROBO4 (ENSG00000154133), ROBO3 (ENSG00000154134), NCAM2 (ENSG00000154654), VCAM1 (ENSG00000162692), NFASC (ENSG00000163531), PRTG (ENSG00000166450), ROBO1 (ENSG00000169855), DSCAM (ENSG00000171587), IGDCC3 (ENSG00000174498), DSCAML1 (ENSG00000177103), CNTN2 (ENSG00000184144), ROBO2 (ENSG00000185008), VSIG10L (ENSG00000186806), DCC (ENSG00000187323), L1CAM (ENSG00000198910)

Protein

Protein identifiers

V-set and immunoglobulin domain-containing protein 10 — Q8N0Z9 (reviewed: Q8N0Z9)

All UniProt accessions (2): Q8N0Z9, F5H724

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N0Z9-1	1	yes
Q8N0Z9-2	2

RefSeq proteins (1): NP_061959* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013106	Ig_V-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR051170	Neural/epithelial_adhesion	Family

Pfam: PF07686, PF13927

UniProt features (32 total): glycosylation site 9, disulfide bond 4, domain 4, compositionally biased region 3, region of interest 2, topological domain 2, sequence variant 2, sequence conflict 2, signal peptide 1, chain 1, splice variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N0Z9-F1	77.26	0.54

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 (4): 44–103, 153–201, 245–290, 331–388

Glycosylation sites (9): 39, 46, 70, 108, 138, 171, 180, 198, 326

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 115 (showing top): GOBP_SYNAPSE_ASSEMBLY, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, GOBP_CELL_CELL_ADHESION, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP, GOBP_CELL_JUNCTION_ORGANIZATION, ONKEN_UVEAL_MELANOMA_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, LIAO_METASTASIS, GOBP_CELL_JUNCTION_ASSEMBLY, DOUGLAS_BMI1_TARGETS_UP, LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP, AML1_01, CUI_TCF21_TARGETS_2_DN, GOCC_CELL_CELL_JUNCTION, RGAGGAARY_PU1_Q6

GO Biological Process (2): synapse assembly (GO:0007416), cell-cell adhesion (GO:0098609)

GO Molecular Function (1): cell adhesion molecule binding (GO:0050839)

GO Cellular Component (3): plasma membrane (GO:0005886), cell-cell junction (GO:0005911), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nervous system development	1
cell junction assembly	1
synapse organization	1
cell adhesion	1
protein binding	1
membrane	1
cell periphery	1
anchoring junction	1
cellular anatomical structure	1

Protein interactions and networks

STRING

328 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VSIG10	ANKRD13D	Q6ZTN6	559
VSIG10	LRRC73	Q5JTD7	556
VSIG10	TEPSIN	Q96N21	532
VSIG10	TTC17	Q96AE7	517
VSIG10	ZNF654	Q8IZM8	507
VSIG10	OR2I1	Q8NGU4	481
VSIG10	FAM174A	Q8TBP5	452
VSIG10	ST3GAL5	Q9UNP4	447
VSIG10	HEATR5B	Q9P2D3	434
VSIG10	CELSR1	Q9NYQ6	425
VSIG10	LYPLAL1	Q5VWZ2	420
VSIG10	OR52I2	Q8NH67	419
VSIG10	CCDC144A	A2RUR9	419
VSIG10	MCOLN2	Q8IZK6	414
VSIG10	SHQ1	Q6PI26	413

IntAct

2 interactions, top by confidence:

A	B	Type	Score
P		psi-mi:“MI:0914”(association)	0.350

BioGRID (8): VSIG10 (Positive Genetic), RPL23 (Cross-Linking-MS (XL-MS)), VSIG10 (Co-fractionation), VSIG10 (Co-fractionation), VSIG10 (Co-fractionation), VSIG10 (Co-fractionation), VSIG10 (Co-fractionation), VSIG10 (Affinity Capture-RNA)

ESM2 similar proteins: A0A140LHF2, A2AJ76, A6H8M9, A8T688, D3YXG0, E7FF10, O60500, P0C0L4, P0C0L5, P21709, P35590, P43121, P50895, P55144, P55146, P59996, P85171, Q00657, Q05695, Q06805, Q06806, Q0PMG2, Q13308, Q3UH53, Q53RD9, Q60750, Q62786, Q7Z5N4, Q8BKG3, Q8HW98, Q8IZJ3, Q8N0Z9, Q8NBP7, Q8NDA2, Q8NFP4, Q8TDY8, Q923P0, Q96MS0, Q96NU0, Q96RW7

Diamond homologs: B0CLX4, D3YX43, P35968, Q6GMZ9, Q8N0Z9, Q92626, Q9I7U4, Q8AXC6, O08775

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1600 predictions. Top by Δscore:

Variant	Effect	Δscore
12:118068593:GTCCC:G	acceptor_gain	1.0000
12:118068594:TCCC:T	acceptor_gain	1.0000
12:118068595:CCC:C	acceptor_gain	1.0000
12:118068595:CCCC:C	acceptor_gain	1.0000
12:118068596:CC:C	acceptor_gain	1.0000
12:118068596:CCC:C	acceptor_gain	1.0000
12:118068597:CC:C	acceptor_gain	1.0000
12:118068598:C:CC	acceptor_gain	1.0000
12:118068598:C:T	acceptor_gain	1.0000
12:118068598:CT:C	acceptor_loss	1.0000
12:118068599:T:C	acceptor_loss	1.0000
12:118068606:C:CT	acceptor_gain	1.0000
12:118068606:C:T	acceptor_gain	1.0000
12:118068607:A:T	acceptor_gain	1.0000
12:118079345:CTGAT:C	donor_gain	1.0000
12:118082121:A:AC	donor_gain	1.0000
12:118082122:C:CC	donor_gain	1.0000
12:118082122:CG:C	donor_gain	1.0000
12:118082122:CGCA:C	donor_gain	1.0000
12:118082426:CCGC:C	acceptor_gain	1.0000
12:118082427:CGC:C	acceptor_gain	1.0000
12:118082427:CGCC:C	acceptor_gain	1.0000
12:118082430:C:CG	acceptor_loss	1.0000
12:118095531:A:AC	donor_gain	1.0000
12:118095532:C:CT	donor_gain	1.0000
12:118095553:TGGA:T	donor_gain	1.0000
12:118066692:CAT:C	acceptor_gain	0.9900
12:118066695:C:CC	acceptor_gain	0.9900
12:118068371:GCTTA:G	donor_loss	0.9900
12:118068372:CTTAC:C	donor_loss	0.9900

AlphaMissense

3528 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:118073886:C:A	W344C	0.999
12:118073886:C:G	W344C	0.999
12:118073888:A:G	W344R	0.996
12:118073888:A:T	W344R	0.996
12:118079497:C:A	W258C	0.994
12:118079497:C:G	W258C	0.994
12:118082296:C:A	W165C	0.994
12:118082296:C:G	W165C	0.994
12:118073803:A:G	L372P	0.992
12:118073755:C:G	C388S	0.991
12:118073756:A:T	C388S	0.991
12:118073887:C:G	W344S	0.990
12:118082138:A:G	L218P	0.990
12:118082196:A:C	Y199D	0.990
12:118082298:A:G	W165R	0.990
12:118082298:A:T	W165R	0.990
12:118079402:C:G	C290S	0.988
12:118079403:A:T	C290S	0.988
12:118073754:G:C	C388W	0.987
12:118073755:C:T	C388Y	0.986
12:118082188:A:C	C201W	0.986
12:118082190:A:G	C201R	0.986
12:118082333:C:G	C153S	0.986
12:118082334:A:T	C153S	0.986
12:118082339:A:G	F151S	0.986
12:118073762:A:C	Y386D	0.985
12:118082189:C:G	C201S	0.985
12:118082190:A:T	C201S	0.985
12:118082333:C:T	C153Y	0.985
12:118073756:A:G	C388R	0.984

dbSNP variants (sampled 300 via entrez): RS1000017240 (12:118087112 G>A,T), RS1000168008 (12:118071680 T>C), RS1000189663 (12:118094994 C>T), RS1000275903 (12:118083409 C>T), RS1000310023 (12:118089783 A>T), RS1000320748 (12:118068174 A>C), RS1000322871 (12:118065078 A>C,G), RS1000372762 (12:118092026 G>A), RS1000402438 (12:118097017 C>T), RS1000413850 (12:118096859 C>A,T), RS1000453377 (12:118070297 C>T), RS1000497307 (12:118087304 A>G), RS1000505294 (12:118069953 C>T), RS1000522384 (12:118064948 C>T), RS1000583462 (12:118071237 G>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

4 associations (top):

Study	Trait	p-value
GCST001762_215	Obesity-related traits	8.000000e-06
GCST002472_1	Morphine dose requirement in tonsillectomy and adenoidectomy surgery	3.000000e-07
GCST009377_10	Bone mineral density	5.000000e-07
GCST012015_5	Chronic rhinosinusitis	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005108	arm span
EFO:0007620	volumetric bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	3
entinostat	increases expression, affects cotreatment	2
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	increases expression, affects cotreatment	1
Fulvestrant	affects cotreatment, increases methylation	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Atrazine	increases expression	1
Nickel	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Triclosan	decreases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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