VSIG10L2

Summary

VSIG10L2 (V-set and immunoglobulin domain containing 10 like 2, HGNC:27879) is a protein-coding gene on chromosome 11q24.2, encoding V-set and immunoglobulin domain-containing protein 10-like 2 (P0DP72).

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

Source: NCBI Gene 338667 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001365077

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27879
Approved symbol	VSIG10L2
Name	V-set and immunoglobulin domain containing 10 like 2
Location	11q24.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283703
Ensembl biotype	protein_coding
Entrez	338667

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000638511, ENST00000638636, ENST00000640497, ENST00000686984

RefSeq mRNA: 3 — MANE Select: NM_001365077 NM_001365077, NM_001391971, NM_001391972

CCDS: CCDS91619

Canonical transcript exons

ENST00000686984 — 12 exons

Exon	Start	End
ENSE00003801534	125948305	125948580
ENSE00003802708	125950014	125950289
ENSE00003805430	125947686	125948036
ENSE00003805902	125953400	125953690
ENSE00003806450	125951813	125952073
ENSE00003806536	125950910	125951158
ENSE00003809482	125954087	125954383
ENSE00003811207	125955057	125955179
ENSE00003927579	125955482	125955506
ENSE00003930213	125955615	125955667
ENSE00003932585	125955817	125956319
ENSE00003937497	125946044	125946137

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 80.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0633 / max 18.8028, expressed in 25 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
117485	0.0633	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of abdomen	UBERON:0001416	80.24	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.64	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.27	gold quality
zone of skin	UBERON:0000014	76.83	gold quality
skin of leg	UBERON:0001511	76.54	gold quality
tendon of biceps brachii	UBERON:0008188	75.24	gold quality
vagina	UBERON:0000996	73.83	gold quality
skin of hip	UBERON:0001554	73.06	gold quality
spleen	UBERON:0002106	68.03	gold quality
ectocervix	UBERON:0012249	65.61	gold quality
mammalian vulva	UBERON:0000997	65.20	silver quality
uterine cervix	UBERON:0000002	63.89	gold quality
left uterine tube	UBERON:0001303	63.50	gold quality
palpebral conjunctiva	UBERON:0001812	62.51	silver quality
layer of synovial tissue	UBERON:0007616	62.50	silver quality
synovial joint	UBERON:0002217	62.28	gold quality
penis	UBERON:0000989	62.09	gold quality
endocervix	UBERON:0000458	61.33	gold quality
body of uterus	UBERON:0009853	60.76	gold quality
epithelium of nasopharynx	UBERON:0001951	60.55	gold quality
upper leg skin	UBERON:0004262	59.76	silver quality
smooth muscle tissue	UBERON:0001135	59.44	gold quality
nipple	UBERON:0002030	59.25	gold quality
ventricular zone	UBERON:0003053	59.13	gold quality
vena cava	UBERON:0004087	59.01	gold quality
mucosa of paranasal sinus	UBERON:0005030	58.89	gold quality
apex of heart	UBERON:0002098	58.40	gold quality
lateral nuclear group of thalamus	UBERON:0002736	58.29	gold quality
inferior vagus X ganglion	UBERON:0005363	58.11	gold quality
endothelial cell	CL:0000115	58.03	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.44

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Vsig10l2	ENSMUSG00000098590
rattus_norvegicus	Vsig10l2	ENSRNOG00000055680

Protein

Protein identifiers

V-set and immunoglobulin domain-containing protein 10-like 2 — P0DP72 (reviewed: P0DP72)

All UniProt accessions (3): A0A1W2PP72, A0A8I5KPR9, P0DP72

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (2): NP_001352006, NP_001378900 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR003961	FN3_dom	Domain
IPR007110	Ig-like_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR052598	IgSF_CEA-related	Family

Pfam: PF13927

UniProt features (19 total): domain 6, disulfide bond 5, glycosylation site 3, signal peptide 1, chain 1, compositionally biased region 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DP72-F1	81.97	0.49

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 (5): 56–122, 169–217, 268–308, 435–481, 522–577

Glycosylation sites (3): 376, 602, 628

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 8 (showing top): GOBP_CELL_CELL_ADHESION, GOCC_CELL_CELL_JUNCTION, GOCC_ANCHORING_JUNCTION, chr11q24, GOMF_CELL_ADHESION_MOLECULE_BINDING, GOBP_CELL_ADHESION, GSE1112_HY_CD8AB_VS_HY_CD8AA_THYMOCYTE_RTOC_CULTURE_DN, GSE41867_DAY6_VS_DAY15_LCMV_CLONE13_EFFECTOR_CD8_TCELL_DN

GO Biological Process (1): cell-cell adhesion (GO:0098609)

GO Molecular Function (2): cell adhesion molecule binding (GO:0050839), protein binding (GO:0005515)

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
cell adhesion	1
protein binding	1
binding	1
membrane	1
cell periphery	1
anchoring junction	1
cellular anatomical structure	1

Protein interactions and networks

STRING

188 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VSIG10L2	FOSB	P53539	204
VSIG10L2	RB1CC1	Q8TDY2	166
VSIG10L2	TENM4	Q6N022	166
VSIG10L2	A0A087WXM4	A0A087WXM4	166
VSIG10L2	ZSCAN26	Q16670	166
VSIG10L2	DNLZ	Q5SXM8	164
VSIG10L2	PRDM16	Q9HAZ2	162
VSIG10L2	HDGFL3	Q9Y3E1	162
VSIG10L2	GPR142	Q7Z601	162
VSIG10L2	SPON1	Q9HCB6	160
VSIG10L2	TMEM252	Q8N6L7	156
VSIG10L2	MOS	P00540	135
VSIG10L2	SLITRK4	Q8IW52	133
VSIG10L2	GPR50	Q13585	124
VSIG10L2	MTNR1B	P49286	124
VSIG10L2	MTNR1A	P48039	124
VSIG10L2	H0Y8X5	H0Y8X5	124

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A140LHF2, A6H8M9, A7LCJ3, A8E0Y8, D3YX43, D3YZF7, O14498, O15197, O70394, O70540, P01877, P0C0K6, P0C788, P0DP72, P35590, P40223, P43121, P50895, P70289, Q00657, Q06418, Q06805, Q15109, Q28173, Q5BK54, Q5NVQ6, Q5TJE4, Q61790, Q61826, Q62151, Q62230, Q63495, Q64612, Q6UVK1, Q6UWB1, Q7Z442, Q86VR7, Q8IZF5, Q8R2Y2, Q8VHY0

Diamond homologs: A0A140LHF2, P0DP72, P11464, P16573, P31809, P31997, P35329, Q00887, Q15223, Q15746, Q16557, Q58EX2, Q6V4S5, Q96FE5, Q9D1T0, Q9GL76, Q9N008, P20273, Q5RDJ4, Q925P2, A0A0B4J1L0, A8MVW5, D3ZQE1, E9QA28, O75871, P06731, P11465, P13688, P40198, P40199, Q00888, Q00889, Q13046, Q14002, Q15238, Q2WEN9, Q3KPI0, Q61400, Q63111, Q810J1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

5053 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:125954163:G:C	W621C	0.990
11:125954163:G:T	W621C	0.990
11:125954194:T:C	F632L	0.989
11:125954196:C:A	F632L	0.989
11:125954196:C:G	F632L	0.989
11:125951922:G:C	W448C	0.987
11:125951922:G:T	W448C	0.987
11:125954195:T:C	F632S	0.986
11:125950144:G:C	W280C	0.984
11:125950144:G:T	W280C	0.984
11:125954244:G:C	W648C	0.984
11:125954244:G:T	W648C	0.984
11:125951013:G:C	W363C	0.983
11:125951013:G:T	W363C	0.983
11:125954323:T:C	F675L	0.983
11:125954325:C:A	F675L	0.983
11:125954325:C:G	F675L	0.983
11:125951889:G:C	W437C	0.982
11:125951889:G:T	W437C	0.982
11:125953509:G:C	W535C	0.982
11:125953509:G:T	W535C	0.982
11:125954324:T:C	F675S	0.982
11:125948417:G:C	W182C	0.980
11:125948417:G:T	W182C	0.980
11:125954161:T:A	W621R	0.980
11:125954161:T:C	W621R	0.980
11:125952014:T:G	F479C	0.979
11:125954327:G:C	R676P	0.979
11:125948534:C:A	N221K	0.978
11:125948534:C:G	N221K	0.978

dbSNP variants (sampled 300 via entrez): RS1000047557 (11:125947628 G>A), RS1000114118 (11:125948596 G>A), RS1000181197 (11:125948967 T>C), RS1000397348 (11:125947339 G>A), RS1000780221 (11:125948039 G>A), RS1000788111 (11:125955853 C>T), RS1001616348 (11:125951305 C>T), RS1001823729 (11:125946761 C>G,T), RS1002186079 (11:125954852 A>G), RS1002394139 (11:125950268 A>G), RS1002413777 (11:125944458 G>T), RS1002433512 (11:125955064 C>T), RS1002466696 (11:125954881 C>G,T), RS1002615973 (11:125950198 T>C), RS1002740598 (11:125945397 G>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

1 associations (top):

Study	Trait	p-value
GCST90000025_1010	Appendicular lean mass	7.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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