VSIG10L

Summary

VSIG10L (V-set and immunoglobulin domain containing 10 like, HGNC:27111) is a protein-coding gene on chromosome 19q13.41, encoding V-set and immunoglobulin domain-containing protein 10-like (Q86VR7).

Located in nucleoplasm.

Source: NCBI Gene 147645 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 118 total
• MANE Select transcript: NM_001163922

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27111
Approved symbol	VSIG10L
Name	V-set and immunoglobulin domain containing 10 like
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000186806
Ensembl biotype	protein_coding
OMIM	617740
Entrez	147645

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000335624, ENST00000600663, ENST00000915571

RefSeq mRNA: 1 — MANE Select: NM_001163922 NM_001163922

CCDS: CCDS54300

Canonical transcript exons

ENST00000335624 — 10 exons

Exon	Start	End
ENSE00001338473	51340015	51340299
ENSE00002202972	51340433	51340726
ENSE00002229801	51341153	51342007
ENSE00002280546	51342085	51342139
ENSE00003112741	51331541	51332640
ENSE00003507226	51338888	51339142
ENSE00003564614	51337930	51338208
ENSE00003567415	51334191	51334304
ENSE00003588028	51337238	51337534
ENSE00003673985	51333791	51333945

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 99.27.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.0416 / max 288.8359, expressed in 108 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182383	0.8902	78
182385	0.1441	47
182384	0.0073	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	99.27	gold quality
esophagus squamous epithelium	UBERON:0006920	98.54	gold quality
esophagus mucosa	UBERON:0002469	96.54	gold quality
pharyngeal mucosa	UBERON:0000355	96.50	gold quality
gingiva	UBERON:0001828	95.96	gold quality
gingival epithelium	UBERON:0001949	95.55	gold quality
oral cavity	UBERON:0000167	94.96	gold quality
upper arm skin	UBERON:0004263	91.69	gold quality
mammalian vulva	UBERON:0000997	88.36	gold quality
skin of leg	UBERON:0001511	88.30	gold quality
body of tongue	UBERON:0011876	88.01	gold quality
skin of abdomen	UBERON:0001416	87.60	gold quality
vagina	UBERON:0000996	87.51	gold quality
penis	UBERON:0000989	86.94	gold quality
zone of skin	UBERON:0000014	86.91	gold quality
parotid gland	UBERON:0001831	86.50	gold quality
esophagus	UBERON:0001043	86.12	gold quality
tonsil	UBERON:0002372	85.12	gold quality
mouth mucosa	UBERON:0003729	83.26	gold quality
saliva-secreting gland	UBERON:0001044	83.02	gold quality
minor salivary gland	UBERON:0001830	81.30	gold quality
pancreatic ductal cell	CL:0002079	81.08	silver quality
buccal mucosa cell	CL:0002336	80.70	gold quality
upper leg skin	UBERON:0004262	79.46	gold quality
ectocervix	UBERON:0012249	78.81	gold quality
sperm	CL:0000019	78.13	gold quality
tongue	UBERON:0001723	78.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.40	gold quality
left ovary	UBERON:0002119	74.75	gold quality
right ovary	UBERON:0002118	74.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting VSIG10L, 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-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-6743-5P	99.48	63.60	721

Literature-anchored findings (GeneRIF, showing 1)

• VSIG10L is a candidate familial Barrett esophagus susceptibility gene, with a putative role in maintaining normal esophageal homeostasis. (PMID:27467440)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Vsig10l	ENSMUSG00000070604
rattus_norvegicus	Vsig10l	ENSRNOG00000023411

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), VSIG10 (ENSG00000176834), DSCAML1 (ENSG00000177103), CNTN2 (ENSG00000184144), ROBO2 (ENSG00000185008), DCC (ENSG00000187323), L1CAM (ENSG00000198910)

Protein

Protein identifiers

V-set and immunoglobulin domain-containing protein 10-like — Q86VR7 (reviewed: Q86VR7)

All UniProt accessions (1): Q86VR7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Expressed in the esophagus, particularly in the suprabasilar layers of the epithelium. Expression is largely reduced in esophageal metaplasia, dysplasia, and adenocarcinoma lesions.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86VR7-1	1	yes
Q86VR7-2	2

RefSeq proteins (1): NP_001157394* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050831	CEA_cell_adhesion	Family

Pfam: PF07679, PF13895

UniProt features (31 total): glycosylation site 8, sequence variant 6, compositionally biased region 4, region of interest 3, topological domain 2, disulfide bond 2, domain 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-Q86VR7-F1	70.18	0.37

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): 324–378, 428–471

Glycosylation sites (8): 32, 88, 96, 144, 423, 487, 641, 650

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): LIAO_METASTASIS, HAMAI_APOPTOSIS_VIA_TRAIL_DN, VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHYLA_CBFA2T3_TARGETS_UP, PEDRIOLI_MIR31_TARGETS_UP, DACH1_TARGET_GENES, RBM34_TARGET_GENES, SKIL_TARGET_GENES, SUPT16H_TARGET_GENES, ZNF354B_TARGET_GENES, ZNF436_TARGET_GENES, ZNF592_TARGET_GENES, MIR4728_5P, MIR6785_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleoplasm (GO:0005654), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
nuclear lumen	1

Protein interactions and networks

STRING

616 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VSIG10L	MORN5	Q5VZ52	464
VSIG10L	ZSCAN26	Q16670	453
VSIG10L	MAPDA	Q6DHV7	414
VSIG10L	KIZ	Q2M2Z5	409
VSIG10L	TCHHL1	Q5QJ38	405
VSIG10L	SHROOM1	Q2M3G4	404
VSIG10L	ZNF835	Q9Y2P0	403
VSIG10L	CHD3	Q12873	392
VSIG10L	NBPF9	P0DPF3	376
VSIG10L	ANKRD36B	Q8N2N9	376
VSIG10L	TEX15	Q9BXT5	368
VSIG10L	CNTNAP3B	Q96NU0	366
VSIG10L	ZNF480	Q8WV37	358
VSIG10L	PHETA1	Q8N4B1	348
VSIG10L	DBNDD1	Q9H9R9	348

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CDH1	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (2): VSIG10L (Proximity Label-MS), VSIG10L (Positive Genetic)

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: D3YZF7, Q28173, Q86VR7, A2ASS6, P05362, P13597, P13598, P13688, P32942, P33729, P35330, Q00238, Q00888, Q00889, Q13046, Q1WIM1, Q28125, Q28730, Q28806, Q4VA61, Q5NKU6, Q5NKV1, Q5NKV2, Q5NKV4, Q5NKV6, Q5NKV9, Q60625, Q8NFZ8, Q8R464, Q8TD84, Q95132, Q9ERM2, Q9UMF0, A0A140LHF2, Q9D2Z1, A0A0B4J1L0, A8MTB9, D3ZQE1, E9QA28, P06731

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	101
Likely benign	6
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1528 predictions. Top by Δscore:

Variant	Effect	Δscore
19:51333789:A:AC	donor_gain	1.0000
19:51333790:C:CC	donor_gain	1.0000
19:51333941:CTTTC:C	acceptor_gain	1.0000
19:51333942:TTTC:T	acceptor_gain	1.0000
19:51333946:C:A	acceptor_loss	1.0000
19:51333950:T:C	acceptor_gain	1.0000
19:51333950:T:TC	acceptor_gain	1.0000
19:51333958:C:CT	acceptor_gain	1.0000
19:51333959:A:T	acceptor_gain	1.0000
19:51334190:CCA:C	donor_gain	1.0000
19:51334305:C:CC	acceptor_gain	1.0000
19:51334315:C:CT	acceptor_gain	1.0000
19:51340429:TCAC:T	donor_loss	1.0000
19:51340430:CACAG:C	donor_loss	1.0000
19:51340431:A:AC	donor_gain	1.0000
19:51340431:ACAGA:A	donor_loss	1.0000
19:51340432:C:CC	donor_gain	1.0000
19:51340460:C:A	donor_gain	1.0000
19:51340727:C:CC	acceptor_gain	1.0000
19:51333783:ACAC:A	donor_loss	0.9900
19:51333785:ACTC:A	donor_loss	0.9900
19:51333786:CT:C	donor_loss	0.9900
19:51333787:T:TC	donor_loss	0.9900
19:51333788:C:CC	donor_loss	0.9900
19:51333789:A:C	donor_loss	0.9900
19:51333790:C:CG	donor_loss	0.9900
19:51333943:TTC:T	acceptor_gain	0.9900
19:51333944:TC:T	acceptor_gain	0.9900
19:51333945:CCTGA:C	acceptor_gain	0.9900
19:51333946:C:CC	acceptor_gain	0.9900

AlphaMissense

5460 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:51340169:C:A	W440C	0.999
19:51340169:C:G	W440C	0.999
19:51339066:C:A	W517C	0.998
19:51339066:C:G	W517C	0.998
19:51340171:A:G	W440R	0.998
19:51340171:A:T	W440R	0.998
19:51338099:C:A	W613C	0.997
19:51338099:C:G	W613C	0.997
19:51340206:C:G	C428S	0.997
19:51340207:A:T	C428S	0.997
19:51340614:C:A	W336C	0.996
19:51340614:C:G	W336C	0.996
19:51340077:C:G	C471S	0.994
19:51340078:A:T	C471S	0.994
19:51340207:A:G	C428R	0.994
19:51340076:G:C	C471W	0.993
19:51340077:C:T	C471Y	0.993
19:51340212:A:G	L426S	0.993
19:51339034:A:C	F528C	0.992
19:51339073:C:G	C515S	0.992
19:51339074:A:T	C515S	0.992
19:51339079:A:G	F513S	0.992
19:51340205:G:C	C428W	0.992
19:51340206:C:T	C428Y	0.992
19:51337476:C:A	W689C	0.991
19:51337476:C:G	W689C	0.991
19:51337478:A:G	W689R	0.991
19:51337478:A:T	W689R	0.991
19:51338935:C:G	C561S	0.991
19:51338936:A:G	C561R	0.991

dbSNP variants (sampled 300 via entrez): RS1000066887 (19:51332464 A>G), RS1000151973 (19:51336565 A>G), RS1000458011 (19:51339923 C>T), RS1000475999 (19:51331377 T>C), RS1000488922 (19:51339532 C>A), RS1000667553 (19:51333892 G>A,C), RS1000978583 (19:51343828 A>C), RS1001142013 (19:51333542 AAGAG>A,AAG,AAGAGAG), RS1001155556 (19:51343093 C>T), RS1001253020 (19:51336903 A>C,G,T), RS1001742054 (19:51335098 C>T), RS1002068397 (19:51335480 A>G), RS1002082188 (19:51332062 G>A,T), RS1002255545 (19:51338176 C>A,G,T), RS1002307809 (19:51338378 T>C)

Disease associations

OMIM: gene MIM:617740 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	affects expression, increases methylation	2
bisphenol F	decreases methylation	1
sodium arsenate	decreases expression, increases abundance	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
hydroquinone	increases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	increases expression, affects cotreatment	1
Estradiol	affects cotreatment, increases expression	1
Niclosamide	increases expression	1
Quercetin	increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Thimerosal	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	increases expression	1
Palmitic Acid	decreases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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