VSIG2

Summary

VSIG2 (V-set and immunoglobulin domain containing 2, HGNC:17149) is a protein-coding gene on chromosome 11q24.2, encoding V-set and immunoglobulin domain-containing protein 2 (Q96IQ7).

Predicted to be involved in lipid metabolic process. Predicted to be located in plasma membrane.

Source: NCBI Gene 23584 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 75 total
• MANE Select transcript: NM_014312

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17149
Approved symbol	VSIG2
Name	V-set and immunoglobulin domain containing 2
Location	11q24.2
Locus type	gene with protein product
Status	Approved
Aliases	CTXL, CTH
Ensembl gene	ENSG00000019102
Ensembl biotype	protein_coding
OMIM	606011
Entrez	23584

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000326621, ENST00000403470, ENST00000896672, ENST00000896673, ENST00000896674

RefSeq mRNA: 2 — MANE Select: NM_014312 NM_001329920, NM_014312

CCDS: CCDS8452, CCDS86258

Canonical transcript exons

ENST00000326621 — 7 exons

Exon	Start	End
ENSE00000749309	124751423	124751580
ENSE00000749310	124750714	124750921
ENSE00000815447	124749708	124749866
ENSE00001014309	124748390	124748534
ENSE00001014311	124748644	124748763
ENSE00001133540	124747474	124747667
ENSE00001249265	124752077	124752255

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 98.58.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8597 / max 646.1237, expressed in 95 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122955	0.5975	51
122956	0.2417	74
122957	0.0204	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	98.58	gold quality
mucosa of transverse colon	UBERON:0004991	98.55	gold quality
rectum	UBERON:0001052	97.83	gold quality
nasal cavity epithelium	UBERON:0005384	97.23	gold quality
buccal mucosa cell	CL:0002336	96.08	gold quality
amniotic fluid	UBERON:0000173	95.04	gold quality
pylorus	UBERON:0001166	94.50	gold quality
left lobe of thyroid gland	UBERON:0001120	94.48	gold quality
right lobe of thyroid gland	UBERON:0001119	94.27	gold quality
colonic mucosa	UBERON:0000317	93.84	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.64	gold quality
thyroid gland	UBERON:0002046	93.46	gold quality
lower esophagus mucosa	UBERON:0035834	93.39	gold quality
monocyte	CL:0000576	93.27	gold quality
body of stomach	UBERON:0001161	92.69	gold quality
epithelial cell of pancreas	CL:0000083	92.66	gold quality
stomach	UBERON:0000945	92.63	gold quality
leukocyte	CL:0000738	92.34	gold quality
mucosa of stomach	UBERON:0001199	91.87	gold quality
transverse colon	UBERON:0001157	91.81	gold quality
palpebral conjunctiva	UBERON:0001812	91.79	gold quality
upper lobe of left lung	UBERON:0008952	91.23	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.17	gold quality
right uterine tube	UBERON:0001302	90.80	gold quality
tendon of biceps brachii	UBERON:0008188	90.16	gold quality
upper lobe of lung	UBERON:0008948	90.09	gold quality
right lung	UBERON:0002167	89.86	gold quality
fundus of stomach	UBERON:0001160	89.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.62	gold quality
cardia of stomach	UBERON:0001162	89.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-114	yes	55.55
E-GEOD-125970	yes	46.46
E-HCAD-10	yes	16.04
E-MTAB-8410	yes	15.35
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation. (PMID:37626304)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Vsig2	ENSMUSG00000001943
rattus_norvegicus	Vsig2	ENSRNOG00000033490

Paralogs (14): VSIG1 (ENSG00000101842), VSIR (ENSG00000107738), GPA33 (ENSG00000143167), IGSF11 (ENSG00000144847), ESAM (ENSG00000149564), CXADR (ENSG00000154639), JAM2 (ENSG00000154721), F11R (ENSG00000158769), MXRA8 (ENSG00000162576), JAM3 (ENSG00000166086), CLMP (ENSG00000166250), MUC15 (ENSG00000169550), VSTM2B (ENSG00000187135), VSIG8 (ENSG00000243284)

Protein

Protein identifiers

V-set and immunoglobulin domain-containing protein 2 — Q96IQ7 (reviewed: Q96IQ7)

Alternative names: Cortical thymocyte-like protein

All UniProt accessions (1): Q96IQ7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Highly expressed in stomach, colon, prostate, trachea and thyroid glands and weakly in bladder and lung.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96IQ7-1	1	yes
Q96IQ7-2	2

RefSeq proteins (2): NP_001316849, NP_055127* (*=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
IPR042475	VSIG2	Family

Pfam: PF07686, PF13927

UniProt features (20 total): sequence conflict 6, glycosylation site 2, disulfide bond 2, topological domain 2, domain 2, signal peptide 1, chain 1, splice variant 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96IQ7-F1	80.30	0.57

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): 45–121, 166–217

Glycosylation sites (2): 206, 138

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 346 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, MULLIGHAN_NPM1_SIGNATURE_3_UP, HNF3ALPHA_Q6, DORSAM_HOXA9_TARGETS_UP, GOBP_PROTEIN_HOMOTETRAMERIZATION, GOBP_RESPONSE_TO_PEPTIDE, RORA1_01, GOBP_REGULATION_OF_SMOOTH_MUSCLE_CELL_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_MUSCLE_CELL_DIFFERENTIATION, ENK_UV_RESPONSE_KERATINOCYTE_UP, GOBP_SMOOTH_MUSCLE_CELL_DIFFERENTIATION, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN

GO Biological Process (1): lipid metabolic process (GO:0006629)

GO Molecular Function (0):

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

698 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VSIG2	CYP27A1	Q02318	784
VSIG2	HSF4	Q9ULV5	770
VSIG2	IGSF9	Q9P2J2	451
VSIG2	GFUS	Q13630	437
VSIG2	LRRC20	Q8TCA0	417
VSIG2	SPA17	Q15506	361
VSIG2	OCLN	Q16625	358
VSIG2	PPP1R14D	Q9NXH3	358
VSIG2	DIPK1A	Q5T7M9	346
VSIG2	PRSS8	Q16651	327
VSIG2	BCL2L15	Q5TBC7	321
VSIG2	VSIG4	Q9Y279	321
VSIG2	TJP1	Q07157	303
VSIG2	PGBD4	Q96DM1	300
VSIG2	GPA33	Q99795	298

IntAct

4 interactions, top by confidence:

A	B	Type	Score
VSIG2	TTI1	psi-mi:“MI:0914”(association)	0.530
VSIG2	TNPO2	psi-mi:“MI:0914”(association)	0.350

BioGRID (80): TNPO2 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), THADA (Affinity Capture-MS), XPO6 (Affinity Capture-MS), IPO7 (Affinity Capture-MS), XPO5 (Affinity Capture-MS), KIF14 (Affinity Capture-MS), ATR (Affinity Capture-MS), SAAL1 (Affinity Capture-MS), TTI1 (Affinity Capture-MS), KIAA1524 (Affinity Capture-MS), COG6 (Affinity Capture-MS), CSE1L (Affinity Capture-MS), XPO4 (Affinity Capture-MS), LEMD3 (Affinity Capture-MS)

ESM2 similar proteins: A0A5B9, A6NDV4, A6QLK4, B1AWJ5, E9PTA2, O75051, O94759, P01850, P01851, P01852, P01857, P01859, P01860, P01861, P01869, P01870, P01906, P01909, P03987, P06333, P0DSE2, P0DTU4, P11364, P15151, P15981, P20759, P20762, P32506, P54900, Q1WIM1, Q1WIM3, Q3TMX7, Q6P767, Q6ZRP7, Q7TQ33, Q812F8, Q8N126, Q8NFZ8, Q8R143, Q8R464

Diamond homologs: A0A075B6I3, A0A075B6I7, A0A075B6J1, A0A075B6K6, A0A075B6P5, A0A075B6T6, A0A075B6T7, A0A075B6T8, A0A075B6U4, A0A075B6V5, A0A075B6W5, A0A075B6X5, A0A087WSX0, A0A087WSZ0, A0A087WT01, A0A087WT02, A0A087WW87, A0A0A0MS06, A0A0A6YYK1, A0A0A6YYK6, A0A0B4J234, A0A0B4J235, A0A0B4J238, A0A0B4J240, A0A0B4J241, A0A0B4J244, A0A0B4J245, A0A0B4J248, A0A0B4J249, A0A0B4J263, A0A0B4J266, A0A0B4J271, A0A0B4J272, A0A0B4J274, A0A0B4J275, A0A0B4J277, A0A0B4J279, A0A0B4J280, A0A0G2JS06, A0A1B0GX51

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3212 predictions. Top by Δscore:

Variant	Effect	Δscore
11:124749867:C:CC	acceptor_gain	1.0000
11:124750712:AC:A	donor_gain	1.0000
11:124750713:CC:C	donor_gain	1.0000
11:124750921:TC:T	acceptor_loss	1.0000
11:124750923:T:A	acceptor_loss	1.0000
11:124751417:G:C	donor_gain	1.0000
11:124751421:A:AC	donor_gain	1.0000
11:124751422:C:CC	donor_gain	1.0000
11:124752076:CCA:C	donor_gain	1.0000
1:70415954:AG:A	acceptor_gain	1.0000
1:70415955:GG:G	acceptor_gain	1.0000
1:70416026:GGGC:G	donor_gain	1.0000
1:70416027:GGC:G	donor_gain	1.0000
1:70416028:GC:G	donor_gain	1.0000
1:70416029:C:G	donor_gain	1.0000
1:70416033:GTACT:G	donor_gain	1.0000
1:70416037:TG:T	donor_loss	1.0000
1:70416038:G:GC	donor_loss	1.0000
1:70416038:G:GG	donor_gain	1.0000
1:70416039:T:TC	donor_loss	1.0000
1:70416040:AA:A	donor_loss	1.0000
1:70416041:A:AC	donor_loss	1.0000
1:70421544:ATCT:A	acceptor_gain	1.0000
1:70421547:T:TA	acceptor_gain	1.0000
1:70421558:T:TA	acceptor_gain	1.0000
1:70421563:CA:C	acceptor_loss	1.0000
1:70421565:G:GC	acceptor_loss	1.0000
1:70421671:CCAAG:C	donor_loss	1.0000
1:70421672:CAAG:C	donor_loss	1.0000
1:70421673:AAG:A	donor_loss	1.0000

AlphaMissense

2078 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:124749757:C:A	W179C	0.999
11:124749757:C:G	W179C	0.999
11:124748700:C:G	C217S	0.996
11:124748701:A:T	C217S	0.996
11:124749759:A:G	W179R	0.996
11:124749759:A:T	W179R	0.996
11:124750779:C:G	C121S	0.996
11:124750780:A:T	C121S	0.996
11:124751467:A:G	W59R	0.996
11:124751467:A:T	W59R	0.996
11:124748701:A:G	C217R	0.995
11:124749797:C:G	C166S	0.995
11:124749798:A:T	C166S	0.995
11:124750780:A:G	C121R	0.995
11:124750786:A:C	Y119D	0.995
11:124749798:A:G	C166R	0.994
11:124750778:G:C	C121W	0.994
11:124750779:C:T	C121Y	0.993
11:124748745:A:G	L202P	0.992
11:124748687:G:C	N221K	0.991
11:124748687:G:T	N221K	0.991
11:124748699:A:C	C217W	0.991
11:124748700:C:T	C217Y	0.991
11:124751465:C:A	W59C	0.991
11:124751465:C:G	W59C	0.991
11:124748707:A:C	Y215D	0.990
11:124749796:G:C	C166W	0.989
11:124750824:A:G	L106P	0.987
11:124749797:C:T	C166Y	0.986
11:124750725:A:G	L139P	0.986

dbSNP variants (sampled 300 via entrez): RS1000544566 (11:124752475 G>A), RS1000573348 (11:124749981 G>C,T), RS1002037989 (11:124749471 C>A,G,T), RS1002778550 (11:124753122 C>T), RS1003102655 (11:124747814 T>TC), RS1003156524 (11:124753442 A>C,G), RS1003440187 (11:124748152 C>A,G), RS1003540411 (11:124753352 G>C), RS1003656650 (11:124752881 T>C), RS1003753663 (11:124751853 T>C), RS1004148251 (11:124753460 C>G), RS1004191103 (11:124751632 G>A,C), RS1005145758 (11:124751958 C>A,T), RS1005559891 (11:124750540 T>TG), RS1005661573 (11:124749608 A>G)

Disease associations

OMIM: gene MIM:606011 | 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
GCST002539_10	Schizophrenia	3.000000e-12
GCST004521_214	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST006803_11	Schizophrenia	2.000000e-15
GCST009600_127	Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
CGP 52608	affects binding, increases reaction	1
theaflavin-3,3’-digallate	affects expression	1
Resveratrol	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Atrazine	increases expression	1
Quercetin	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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