LUM

Summary

LUM (lumican, HGNC:6724) is a protein-coding gene on chromosome 12q21.33, encoding Lumican (P51884).

This gene encodes a member of the small leucine-rich proteoglycan (SLRP) family that includes decorin, biglycan, fibromodulin, keratocan, epiphycan, and osteoglycin. In these bifunctional molecules, the protein moiety binds collagen fibrils and the highly charged hydrophilic glycosaminoglycans regulate interfibrillar spacings. Lumican is the major keratan sulfate proteoglycan of the cornea but is also distributed in interstitial collagenous matrices throughout the body. Lumican may regulate collagen fibril organization and circumferential growth, corneal transparency, and epithelial cell migration and tissue repair.

Source: NCBI Gene 4060 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 34 total
• MANE Select transcript: NM_002345

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6724
Approved symbol	LUM
Name	lumican
Location	12q21.33
Locus type	gene with protein product
Status	Approved
Aliases	SLRR2D
Ensembl gene	ENSG00000139329
Ensembl biotype	protein_coding
OMIM	600616
Entrez	4060

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000266718, ENST00000546642, ENST00000548071, ENST00000891368, ENST00000891369, ENST00000963638

RefSeq mRNA: 1 — MANE Select: NM_002345 NM_002345

CCDS: CCDS9038

Canonical transcript exons

ENST00000266718 — 3 exons

Exon	Start	End
ENSE00000937597	91108118	91109000
ENSE00001374163	91111398	91111494
ENSE00002408674	91102629	91104319

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 99.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 155.3227 / max 4649.2960, expressed in 1024 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
132551	114.1151	1005
132550	34.7157	795
132552	6.4301	730
132549	0.0618	22

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gall bladder	UBERON:0002110	99.94	gold quality
mucosa of paranasal sinus	UBERON:0005030	99.91	gold quality
calcaneal tendon	UBERON:0003701	99.89	gold quality
synovial joint	UBERON:0002217	99.80	gold quality
tibia	UBERON:0000979	99.78	gold quality
visceral pleura	UBERON:0002401	99.77	gold quality
superficial temporal artery	UBERON:0001614	99.70	gold quality
mammary duct	UBERON:0001765	99.66	gold quality
tendon of biceps brachii	UBERON:0008188	99.65	gold quality
vena cava	UBERON:0004087	99.64	gold quality
periodontal ligament	UBERON:0008266	99.64	gold quality
decidua	UBERON:0002450	99.53	gold quality
lower lobe of lung	UBERON:0008949	99.51	gold quality
stromal cell of endometrium	CL:0002255	99.48	gold quality
skin of hip	UBERON:0001554	99.48	gold quality
penis	UBERON:0000989	99.45	gold quality
right coronary artery	UBERON:0001625	99.43	gold quality
endocervix	UBERON:0000458	99.41	gold quality
mucosa of urinary bladder	UBERON:0001259	99.40	gold quality
peritoneum	UBERON:0002358	99.40	gold quality
adipose tissue of abdominal region	UBERON:0007808	99.40	gold quality
upper lobe of lung	UBERON:0008948	99.40	gold quality
omental fat pad	UBERON:0010414	99.40	gold quality
upper lobe of left lung	UBERON:0008952	99.39	gold quality
right adrenal gland cortex	UBERON:0035827	99.39	gold quality
myometrium	UBERON:0001296	99.38	gold quality
saphenous vein	UBERON:0007318	99.38	gold quality
cauda epididymis	UBERON:0004360	99.37	gold quality
pylorus	UBERON:0001166	99.35	gold quality
pericardium	UBERON:0002407	99.34	gold quality

Single-cell (SCXA)

Detected in 41 experiment(s), a significant marker in 40.

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	25745.10
E-HCAD-23	yes	23518.77
E-MTAB-6701	yes	21724.78
E-CURD-126	yes	13959.03
E-GEOD-75688	yes	13548.28
E-MTAB-8322	yes	10242.69
E-MTAB-9388	yes	8898.50
E-MTAB-6653	yes	7786.41
E-MTAB-8410	yes	7763.32
E-MTAB-7407	yes	7687.24
E-MTAB-6308	yes	6907.76
E-HCAD-15	yes	5889.68
E-MTAB-10485	yes	5782.36
E-GEOD-75140	yes	5290.79
E-CURD-46	yes	5262.14

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ELF4, GLI2, TP53

miRNA regulators (miRDB)

50 targeting LUM, 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-3924	100.00	72.09	2394
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-4645-3P	99.76	69.33	993
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-519A-3P	99.67	71.67	1868

Literature-anchored findings (GeneRIF, showing 40)

• Expression and accumulation of lumican protein in uterine cervical cancer (PMID:11956587)
• the lumican protein synthesized by cancer cells, fibroblasts and epithelial cells with mild reactive dysplasia found adjacent to cancer cells may affect the growth of human colorectal cancer cells. (PMID:12366811)
• Lumican protein has an inhibitory effect on HEK 293 cell growth in vitro. (PMID:14720136)
• Inverse regulation in the expression of endoglin and lumican. (PMID:14996436)
• studies of lumican-transfected melanoma cells suggest that lumican is involved in the control melanoma growth and invasion and may be considered, like decorin, as an anti-tumor factor from the extracellular matrix (PMID:15149859)
• Malignant cells can actively influence the composition of the extracellular matrix through TGFbeta1 and other soluble factors. (PMID:15336555)
• No evidence that endothelial dysfunction and germline mutation of lumican and keratocan genes participate in the etiology of subepithelial corneal haze. (PMID:16760896)
• An SNP (rs3759223), which is located in the promoter region of the lumican gene, may be worth further investigation to determine its association with development of high myopia. (PMID:16902402)
• metastatic melanoma cell lines were found to express lumican mRNA and effectively secrete lumican in a proteoglycan form, characterized to be substituted mostly with keratan sulfate chains; lumican mRNA was not detected in normal melanocytes (PMID:17050378)
• In addition, no pathogenic sequence variations were found in DCN, DSPG3, LUM, PITX2 and FOXC1, which have also been implicated in corneal and anterior segment dysgenesis. (PMID:17558846)
• Lumican expression in stromal tissues plays an important role in the growth and invasion of pancreatic cancer. (PMID:17671699)
• lumican expression may be positively correlated with the differentiation and negatively correlated with the progression of osteosarcoma (PMID:18093185)
• Lumican induces cell migration by activating ERK 1/2 signaling and ERK 1/2 stimulates expression of integrin beta1. (PMID:18477477)
• Multiple core-protein species were detected for decorin, biglycan, lumican and keratocan in the degenerate osteoarthritic articular cartilage and menisci. (PMID:18620607)
• Homologous sequence in lumican and fibromodulin leucine-rich repeat 5-7 competes for collagen binding. (PMID:19008226)
• the transcripts upregulated according to disease progression were associated with signaling pathway/transcription, including tumor-associated calcium signal transducer 1 and chemokine ligand 19, and with cell communication, such as collagen. (PMID:19012040)
• Expression and roles of lumican in lung adenocarcinoma and squamous cell carcinoma. (PMID:19020750)
• Genetic variation in lumican gene is associated with breast cancer. (PMID:19036156)
• The study does not support the association of high myopia with alleles of rs2229336 in TGIF, rs3759223 in lumican, rs1982073 in TGFB1, and rs3735520 in HGF. (PMID:19060265)
• Histologically progressive nonalcoholic fatty liver disease is associated with overexpression of lumican. (PMID:19330863)
• the cytoskeleton remodeling and the decreased pFAK phosphorylation induced by lumican in melanoma cells might explain, at least in part, the anti-invasive effect of lumincan (PMID:19394140)
• Data suggest that five novel genes, LUM, PDE3B, PDGF-C, NRG1 and PKD2, have great potential for predicting the efficacy of cisplatin-based chemotherapy against OSCC. (PMID:19569180)
• Genetic variation in the regulatory domains of the lumican gene, where both rs3759223 and rs3741834 are located, are associated with high myopia susceptibility among the Han Chinese. (PMID:19616852)
• These observations suggest that LUM gene polymorphisms contribute to the development of high myopia. (PMID:19643966)
• determined the active sequence of the lumican core protein responsible for the inhibition of melanoma cell migration (PMID:19686741)
• four polymorphisms of the LUM promoter contribute to the pathogenesis of high myopia. (PMID:20010793)
• lumican protein plays important roles in the inhibition of HEK cell attachment and growth, and it might inhibit the activation of integrin pathways (PMID:20138170)
• Linkage and haplotype analyses identified 12q21.33 as a locus for posterior amorphous corneal dystrophy. However, no mutations were identified in the candidate genes (KERA, LUM, DCN, EPYC) within this region. (PMID:20357198)
• lumican may play a key role in the generation of a new collagen network by fibroblast-like cells (PMID:20819773)
• regulates osteosarcoma cell adhesion by modulating TGFbeta2 activity (PMID:21421073)
• Single nucleotide polymorphisms in lumican gene are associated with systemic lupus erythematosus in the Taiwan Chinese Han population. (PMID:21885486)
• lumican and fibromodulin display different behaviors and that lumican may promote regeneration of the TMJ after degeneration and deformation induced by IL-1 beta. (PMID:22073367)
• Lumican may be a potential acute aortic dissection (AAD)-related serum marker that may assist the diagnosis of AAD. (PMID:22228989)
• The reduction in keratan sulfate levels and the strong correlation between chondroitin 6-sulfate and keratan sulfate levels indi-cates suppressed cartilage turnover after arthroscopic surgery. (PMID:22441960)
• Lack of Lumican expression is associated with recurrence in colon cancer. (PMID:22711178)
• LUM in combination with other known markers, such as CRP, could be evaluated as a panel of biomarkers of POAD. (PMID:22721676)
• Our results confirm that the PAX6, Lumican, and MYOC genes were not associated with high myopia in the Han Chinese in Northeastern China. (PMID:22809227)
• lumican expression and its presence in ECM has an impact on colon cancer cells motility and may modulate invasiveness of colon cancer. (PMID:22814255)
• The current study did not support an association between the promoter SNPs of the LUM gene with high myopia in the Korean population. (PMID:23145541)
• lumican present in the reactive stroma surrounding prostate primary tumors plays a restrictive role on cancer progression (PMID:23399832)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lum	ENSDARG00000045580
mus_musculus	Lum	ENSMUSG00000036446
rattus_norvegicus	Lum	ENSRNOG00000004610

Paralogs (10): EPYC (ENSG00000083782), OGN (ENSG00000106809), ECM2 (ENSG00000106823), FMOD (ENSG00000122176), OMG (ENSG00000126861), OMD (ENSG00000127083), KERA (ENSG00000139330), PRELP (ENSG00000188783), LINGO4 (ENSG00000213171), LINGO3 (ENSG00000220008)

Protein

Protein identifiers

Lumican — P51884 (reviewed: P51884)

Alternative names: Keratan sulfate proteoglycan lumican

All UniProt accessions (2): P51884, A0A384N669

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Binds to laminin.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Cornea and other tissues.

Post-translational modifications. Sulfated on tyrosine residue(s). Contains keratan sulfate.

Similarity. Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.

RefSeq proteins (1): NP_002336* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000372	LRRNT	Domain
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050333	SLRP	Family

Pfam: PF13516, PF13855

UniProt features (28 total): repeat 11, modified residue 6, glycosylation site 4, sequence conflict 2, signal peptide 1, chain 1, domain 1, disulfide bond 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P51884-F1	90.70	0.82

Functional residue map

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

Post-translational modifications (6): 19, 20, 21, 23, 30, 304

Disulfide bonds (1): 295–328

Glycosylation sites (4): 88, 127, 160, 252

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

ID	Pathway
R-HSA-2022854	Keratan sulfate biosynthesis
R-HSA-2022857	Keratan sulfate degradation
R-HSA-216083	Integrin cell surface interactions
R-HSA-3000178	ECM proteoglycans
R-HSA-3656225	Defective CHST6 causes MCDC1
R-HSA-3656243	Defective ST3GAL3 causes MCT12 and EIEE15
R-HSA-3656244	Defective B4GALT1 causes B4GALT1-CDG (CDG-2d)
R-HSA-1430728	Metabolism
R-HSA-1474244	Extracellular matrix organization
R-HSA-1630316	Glycosaminoglycan metabolism
R-HSA-1638074	Keratan sulfate/keratin metabolism
R-HSA-1643685	Disease
R-HSA-3560782	Diseases associated with glycosaminoglycan metabolism
R-HSA-3781865	Diseases of glycosylation
R-HSA-5668914	Diseases of metabolism
R-HSA-71387	Metabolism of carbohydrates and carbohydrate derivatives

MSigDB gene sets: 0 (showing top):

GO Biological Process (7): visual perception (GO:0007601), collagen fibril organization (GO:0030199), positive regulation of transforming growth factor beta1 production (GO:0032914), positive regulation of transcription by RNA polymerase II (GO:0045944), cartilage development (GO:0051216), response to growth factor (GO:0070848), response to Aroclor 1254 (GO:1904010)

GO Molecular Function (4): extracellular matrix structural constituent (GO:0005201), collagen binding (GO:0005518), extracellular matrix structural constituent conferring compression resistance (GO:0030021), protein binding (GO:0005515)

GO Cellular Component (7): extracellular region (GO:0005576), fibrillar collagen trimer (GO:0005583), obsolete extracellular space (GO:0005615), Golgi lumen (GO:0005796), extracellular matrix (GO:0031012), lysosomal lumen (GO:0043202), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-9 pathways:

Category	Pathways
Diseases associated with glycosaminoglycan metabolism	3
Keratan sulfate/keratin metabolism	2
Extracellular matrix organization	2
Metabolism of carbohydrates and carbohydrate derivatives	1
Glycosaminoglycan metabolism	1
Diseases of glycosylation	1
Diseases of metabolism	1
Disease	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
sensory perception of light stimulus	1
extracellular matrix organization	1
transforming growth factor beta1 production	1
regulation of transforming growth factor beta1 production	1
positive regulation of transforming growth factor beta production	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
skeletal system development	1
animal organ development	1
connective tissue development	1
response to endogenous stimulus	1
response to chemical	1
structural molecule activity	1
extracellular matrix	1
protein-containing complex binding	1
extracellular matrix structural constituent	1
binding	1
cellular anatomical structure	1
collagen trimer	1
fibrillar collagen complex	1
extracellular protein-containing complex	1
Golgi apparatus	1
intracellular organelle lumen	1
external encapsulating structure	1
lysosome	1
vacuolar lumen	1
extracellular vesicle	1

Protein interactions and networks

STRING

3416 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LUM	FN1	P02751	932
LUM	BGN	P13247	858
LUM	COL1A1	P02452	854
LUM	CHST6	Q9GZX3	852
LUM	DCN	P07585	824
LUM	COL1A2	P02464	817
LUM	POSTN	Q15063	806
LUM	ACAN	P16112	792
LUM	HSPG2	P98160	761
LUM	CHST1	O43916	756
LUM	CHST3	Q7LGC8	749
LUM	DPT	Q07507	740
LUM	COL3A1	P02461	739
LUM	SULT1C4	O75897	729
LUM	SULT1C3	Q6IMI6	729

IntAct

46 interactions, top by confidence:

A	B	Type	Score
LUM	PRKCA	psi-mi:“MI:0915”(physical association)	0.560
LUM	YWHAG	psi-mi:“MI:0915”(physical association)	0.560
LUM	SETDB1	psi-mi:“MI:0915”(physical association)	0.560
LUM	KAT5	psi-mi:“MI:0915”(physical association)	0.560
LMO3	LUM	psi-mi:“MI:0915”(physical association)	0.560
LUM	MMP14	psi-mi:“MI:0194”(cleavage reaction)	0.560
LUM	MMP14	psi-mi:“MI:0407”(direct interaction)	0.560
LGALS1	PODXL	psi-mi:“MI:0914”(association)	0.530
APP	LUM	psi-mi:“MI:0407”(direct interaction)	0.440
RMDN1	LUM	psi-mi:“MI:0915”(physical association)	0.400
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
LUM	GNAQ	psi-mi:“MI:0915”(physical association)	0.370
LUM	CFTR	psi-mi:“MI:0915”(physical association)	0.370
LUM	CTH	psi-mi:“MI:0914”(association)	0.350
LGALS9B	ABCC4	psi-mi:“MI:0914”(association)	0.350
ZNF488	USO1	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
LGALS3	SDCBP	psi-mi:“MI:0914”(association)	0.350
LGALS9	CYB5A	psi-mi:“MI:0914”(association)	0.350

BioGRID (35): LUM (Affinity Capture-MS), LRRC40 (Affinity Capture-MS), THUMPD1 (Affinity Capture-MS), PTPN11 (Affinity Capture-MS), RHOA (Affinity Capture-MS), CTH (Affinity Capture-MS), LUM (Affinity Capture-MS), LUM (Affinity Capture-MS), LUM (Affinity Capture-MS), LUM (Affinity Capture-MS), LUM (Affinity Capture-MS), RSRC1 (Affinity Capture-MS), LUM (Affinity Capture-MS), ACAN (Co-purification), LUM (Biochemical Activity)

ESM2 similar proteins: A0N0X6, A4IIW9, B2LT61, B3Y613, B3Y614, B3Y615, B3Y618, B5T267, O46378, O46379, O60603, O94898, P13605, P50608, P50609, P51884, P51885, P51886, P51890, P58681, Q05443, Q06828, Q0GC71, Q0ZUL9, Q15399, Q2PZH4, Q2V897, Q32Q07, Q3URE9, Q50L44, Q52KR2, Q5R482, Q61809, Q689D1, Q6T752, Q6UXK5, Q6UXM1, Q704V6, Q7L985, Q7TQ62

Diamond homologs: A3KNN3, A4IIW9, A6H789, A6H793, A6NJW4, A8WHP9, E9Q7T7, O46379, O75093, O75094, O88280, O94769, P21793, P24014, P51884, P51885, P51886, P59034, P59035, P83503, Q05443, Q3MHH9, Q5FW85, Q5M7S9, Q65YW8, Q6EMK4, Q6NUI6, Q6R5N8, Q8R5M3, Q8VCH9, Q96PB8, Q9BY71, Q9GKQ6, Q9GZU5, Q9TTE2, Q9WVB4, Q9WVC1, Q9Z0L0, E7FE13, F1MLX5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Signaling by Interleukins	5	11.1×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of cell growth	6	28.9×	2e-05
positive regulation of cell migration	6	9.8×	1e-03
negative regulation of gene expression	5	9.1×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	5
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

217 predictions. Top by Δscore:

Variant	Effect	Δscore
12:91104315:AAACT:A	acceptor_gain	1.0000
12:91104316:AACT:A	acceptor_gain	1.0000
12:91104318:CT:C	acceptor_gain	1.0000
12:91104320:C:CC	acceptor_gain	1.0000
12:91104320:C:T	acceptor_loss	1.0000
12:91104326:A:AC	acceptor_gain	1.0000
12:91104327:T:C	acceptor_gain	1.0000
12:91104327:T:TC	acceptor_gain	1.0000
12:91104321:T:A	acceptor_loss	0.9900
12:91104326:A:C	acceptor_gain	0.9900
12:91108116:A:AC	donor_gain	0.9900
12:91108117:C:CT	donor_gain	0.9900
12:91108117:CT:C	donor_gain	0.9900
12:91108117:CTCT:C	donor_gain	0.9900
12:91104317:ACTCT:A	acceptor_gain	0.9800
12:91104318:CTCT:C	acceptor_gain	0.9800
12:91108116:ACTCT:A	donor_gain	0.9800
12:91108117:CTCTC:C	donor_gain	0.9800
12:91108950:C:CT	acceptor_gain	0.9800
12:91108951:A:T	acceptor_gain	0.9700
12:91111397:CCTTA:C	donor_gain	0.9700
12:91104316:AACTC:A	acceptor_gain	0.9600
12:91104334:A:C	acceptor_gain	0.9600
12:91106400:T:C	donor_gain	0.9600
12:91108112:A:AC	donor_gain	0.9600
12:91108113:C:CC	donor_gain	0.9600
12:91108116:ACT:A	donor_gain	0.9600
12:91108117:CTC:C	donor_gain	0.9600
12:91109001:C:CC	acceptor_gain	0.9600
12:91111393:CTTA:C	donor_loss	0.9600

AlphaMissense

2229 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:91108822:C:T	C53Y	1.000
12:91104253:C:G	R310P	0.999
12:91104298:C:G	C295S	0.999
12:91104299:A:T	C295S	0.999
12:91108189:T:A	N264I	0.999
12:91108198:A:G	L261P	0.999
12:91108204:A:G	L259P	0.999
12:91108276:C:G	R235P	0.999
12:91108279:A:G	L234P	0.999
12:91108539:G:C	N147K	0.999
12:91108539:G:T	N147K	0.999
12:91108540:T:A	N147I	0.999
12:91108555:A:G	L142P	0.999
12:91108602:G:C	N126K	0.999
12:91108602:G:T	N126K	0.999
12:91108603:T:A	N126I	0.999
12:91108618:A:G	L121P	0.999
12:91108680:G:C	N100K	0.999
12:91108680:G:T	N100K	0.999
12:91108696:A:G	L95P	0.999
12:91108762:A:G	L73P	0.999
12:91108768:A:G	L71P	0.999
12:91108821:A:C	C53W	0.999
12:91108822:C:A	C53F	0.999
12:91108822:C:G	C53S	0.999
12:91108823:A:G	C53R	0.999
12:91108823:A:T	C53S	0.999
12:91108858:C:G	C41S	0.999
12:91108859:A:G	C41R	0.999
12:91108859:A:T	C41S	0.999

dbSNP variants (sampled 300 via entrez): RS1000372689 (12:91112781 C>T), RS1000905803 (12:91103437 T>C), RS1001019883 (12:91103138 G>C), RS1001137864 (12:91109763 T>C), RS1001312923 (12:91110173 G>A), RS1001485833 (12:91109406 C>T), RS1001597157 (12:91110316 G>A), RS1001659265 (12:91109893 G>A), RS1001694241 (12:91105170 A>G), RS1001864728 (12:91109916 G>C), RS1001921226 (12:91111278 G>A), RS1003466985 (12:91105249 C>G), RS1003584459 (12:91104810 C>A), RS1004395221 (12:91107031 G>T), RS1004660953 (12:91111529 G>GGA,GGC,GGT)

Disease associations

OMIM: gene MIM:600616 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001784_42	Pulmonary function (smoking interaction)	5.000000e-07
GCST002307_11	Systolic blood pressure (alcohol consumption interaction)	2.000000e-07
GCST002307_4	Systolic blood pressure (alcohol consumption interaction)	2.000000e-07
GCST005580_290	Intraocular pressure	2.000000e-09
GCST006585_640	Blood protein levels	2.000000e-06
GCST009391_669	Metabolite levels	3.000000e-06

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0003892	pulmonary function measurement
EFO:0004713	FEV/FVC ratio
EFO:0004329	alcohol drinking
EFO:0006335	systolic blood pressure
EFO:0004695	intraocular pressure measurement
EFO:0009770	leucine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

87 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases methylation	8
Benzo(a)pyrene	affects methylation, decreases expression, increases expression	4
bisphenol A	decreases methylation, increases expression, affects cotreatment	3
sodium arsenite	increases abundance, decreases expression, affects cotreatment	3
Tetrachlorodibenzodioxin	affects expression, increases expression	3
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	2
Resveratrol	affects cotreatment, increases expression, decreases expression	2
Acetaminophen	decreases expression	2
Cisplatin	affects cotreatment, affects expression, decreases response to substance	2
Copper	affects cotreatment, increases expression, affects binding	2
Dexamethasone	decreases expression, affects cotreatment, increases expression	2
Diethylhexyl Phthalate	affects cotreatment, decreases expression, increases expression	2
Doxorubicin	decreases expression, decreases response to substance	2
Lipopolysaccharides	decreases expression, increases expression, affects response to substance, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Silicon Dioxide	decreases expression, increases expression	2
Tretinoin	increases expression, decreases expression	2
Aflatoxin B1	affects expression, increases expression	2
Paclitaxel	affects cotreatment, affects expression, decreases response to substance	2
bisphenol F	affects cotreatment, increases expression	1
2,4,6-tribromophenol	increases expression	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
decabromobiphenyl ether	increases expression	1
ascorbate-2-phosphate	affects binding, affects cotreatment, increases expression	1
diisononyl phthalate	affects cotreatment, decreases expression	1
sulforaphane	decreases expression	1
lead nitrate	affects cotreatment, decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D6BV	HyCyte JEG-3 KO-hLUM	Cancer cell line	Male

Clinical trials (associated diseases)

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