COLEC11 (collectin subfamily member 11)

Gene

• Entrez ID: 78989
• Gene name: Collectin subfamily member 11
• Gene symbol: COLEC11
• Synonyms (NCBI Gene): 3MC2, CL-11, CL-K1-I, CL-K1-II, CL-K1-IIa, CL-K1-IIb, CLK1
• Chromosome: 2
• Chromosome location: 2p25.3
• Summary: This gene encodes a member of the collectin family of C-type lectins that possess collagen-like sequences and carbohydrate recognition domains. Collectins are secreted proteins that play important roles in the innate immune system by binding to carbohydra

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1572389284	C>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant, non coding transcript variant, upstream transcript variant, genic upstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1920362	hsa-miR-3065-3p	CLIP-seq
MIRT1920363	hsa-miR-3919	CLIP-seq
MIRT1920364	hsa-miR-4756-3p	CLIP-seq
MIRT1920365	hsa-miR-4778-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001867	Process	Complement activation, lectin pathway	IDA	24174618
GO:0001867	Process	Complement activation, lectin pathway	IEA
GO:0001867	Process	Complement activation, lectin pathway	IMP	25912189
GO:0002376	Process	Immune system process	IEA
GO:0002752	Process	Cell surface pattern recognition receptor signaling pathway	NAS	24174618
GO:0003677	Function	DNA binding	IDA	20956340, 23954398
GO:0005509	Function	Calcium ion binding	IDA	25912189
GO:0005515	Function	Protein binding	IPI	20956340, 24174618, 32041782, 32045104
GO:0005537	Function	D-mannose binding	IDA	20956340, 25912189
GO:0005537	Function	D-mannose binding	IEA
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005615	Component	Extracellular space	IBA
GO:0005615	Component	Extracellular space	IDA	25912189
GO:0005615	Component	Extracellular space	NAS	25912189
GO:0006508	Process	Proteolysis	IDA	24174618
GO:0006956	Process	Complement activation	IDA	23954398
GO:0009897	Component	External side of plasma membrane	NAS	25912189
GO:0019730	Process	Antimicrobial humoral response	IDA	20956340
GO:0030246	Function	Carbohydrate binding	IEA
GO:0032502	Process	Developmental process	ISS
GO:0042802	Function	Identical protein binding	IPI	20956340, 24174618
GO:0042806	Function	Fucose binding	IDA	20956340
GO:0045087	Process	Innate immune response	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0070492	Function	Oligosaccharide binding	IDA	25912189
GO:0097194	Process	Execution phase of apoptosis	IC	23954398
GO:0120153	Function	Calcium-dependent carbohydrate binding	IDA	25912189
GO:1903028	Process	Positive regulation of opsonization	IDA	24174618
GO:1903028	Process	Positive regulation of opsonization	IEA
GO:1905370	Component	Serine-type endopeptidase complex	NAS	24174618

Other IDs

• MIM: 612502
• HGNC: 17213
• e!Ensembl: ENSG00000118004

Protein

• UniProt ID: Q9BWP8
• Protein name: Collectin-11 (Collectin kidney protein 1) (CL-K1)
• Protein function: Lectin that plays a role in innate immunity, apoptosis and embryogenesis (PubMed:21258343, PubMed:23954398, PubMed:25912189). Calcium-dependent lectin that binds self and non-self glycoproteins presenting high mannose oligosaccharides with at le
• PDB: 4YLI, 4YMD
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01391	Collagen	21 → 93	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	62 → 116	Collagen triple helix repeat (20 copies)	Repeat
  PF00059	Lectin_C	159 → 266	Lectin C-type domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous (PubMed:17179669). Detected in adrenal gland, kidney, liver, ovaries and testis (at protein level) (PubMed:20956340). {ECO:0000269|PubMed:17179669, ECO:0000269|PubMed:20956340}.
• Sequence:

  MRGNLALVGVLISLAFLSLLPSGHPQPAGDDACSVQILVPGLKGDAGEKGDKGAPGRPGR
  VGPTGEKGDMGDKGQKGSVGRHGKIGPIGSKGEKGDSGDIGPPGPNGEPGLPCECSQLRK
  AIGEMDNQVSQLTSELKFIKNAVAGVRETESKIYLLVKEEKRYADAQLSCQGRGGTLSMP
  KDEAANGLMAAYLAQAGLARVFIGINDLEKEGAFVYSDHSPMRTFNKWRSGEPNNAYDEE
  DCVEMVASGGWNDVACHTTMYFMCEFDKENM

• Sequence length: 271

Pathways

KEGG:

Phagosome

Reactome:

Lectin pathway of complement activation
Initial triggering of complement
Scavenging by Class A Receptors

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
3MC syndrome	Pathogenic	rs2528243821	RCV003994655	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
3MC syndrome 2	Pathogenic	rs387907075, rs1572389284, rs387907076, rs2147975970	RCV000023959 RCV000023960 RCV000023961 RCV000023962	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant tumor of urinary bladder	Pathogenic	rs387907076	RCV005888659	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CARNEVALE SYNDROME	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLEC11-related disorder	Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ABNORMALITIES	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ULNAR RENAL SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALPUECH FACIAL CLEFTING SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULOPALATOSKELETAL SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
3MC syndrome	3MC syndrome	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Accessory nipple	Accessory Nipple	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	34539672	Stimulate	★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases of the Nervous System	Autoimmune nervous system disorder	Pubtator	30286468	Associate	★☆☆☆☆ Found in Text Mining only
Bilateral Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Blepharophimosis	Blepharophimosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	25737553, 34986671	Associate	★☆☆☆☆ Found in Text Mining only
Carnevale syndrome	3MC syndrome	CTD_human_DG	21258343		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carnevale syndrome	3MC syndrome	GENOMICS_ENGLAND_DG	21258343, 2569826, 28301481		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carnevale syndrome	3MC syndrome	UNIPROT_DG	21258343, 25912189, 28301481		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carnevale syndrome	3MC syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	32503434, 37691929	Associate	★☆☆☆☆ Found in Text Mining only
Congenital exomphalos	Congenital Exomphalos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Craniofacial ulnar renal syndrome	Craniofacial Ulnar Renal Syndrome	ORPHANET_DG	21258343		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Craniofacial ulnar renal syndrome	Craniofacial Ulnar Renal Syndrome	BEFREE	22475410, 25912189, 26789649		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Craniosynostosis	Craniosynostosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Development Disorder	BEFREE	25912189		★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	31537649	Associate	★☆☆☆☆ Found in Text Mining only
Disseminated Intravascular Coagulation	Disseminated Intravascular Coagulation	BEFREE	30323815, 30808212		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	32194853	Associate	★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	34539672	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	28581641		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glomerulonephritis IGA	Iga nephropathy	Pubtator	34615657	Associate	★☆☆☆☆ Found in Text Mining only
Graft vs Host Disease	Graft-versus-host disease	Pubtator	18814951	Associate	★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	29606096	Stimulate	★☆☆☆☆ Found in Text Mining only
Incontinentia Pigmenti Achromians	Incontinentia Pigmenti Achromians	CTD_human_DG	21258343		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	29071557		★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	34615657	Associate	★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	33728331	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	27940419, 28581641, 29802995		★☆☆☆☆ Found in Text Mining only
Malpuech facial clefting syndrome	Malpuech Facial Clefting Syndrome	CTD_human_DG	21258343		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malpuech facial clefting syndrome	Malpuech facial clefting syndrome	Pubtator	34636477	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma Cutaneous Malignant	Melanoma	Pubtator	34986671	Associate	★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy, Duchenne	Duchenne Muscular Dystrophy	BEFREE	27940419, 28555643		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	18927074		★☆☆☆☆ Found in Text Mining only
Oculopalatoskeletal syndrome	3MC syndrome	CTD_human_DG	21258343		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Oculopalatoskeletal syndrome	Oculopalatosekeletal syndrome	Pubtator	32441374	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Oral cleft	Oral cleft	HPO_DG			★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	27769915, 29025968		★☆☆☆☆ Found in Text Mining only
Pigmentation Disorders	Pigmentation Disorders	CTD_human_DG	21258343		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	37143720	Associate	★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Radioulnar Synostosis	Radioulnar Synostosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Septicemia	Septicemia	BEFREE	30808212		★☆☆☆☆ Found in Text Mining only
Spina Bifida Occulta	Spina bifida occulta	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	35156507	Associate	★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	29866747		★☆☆☆☆ Found in Text Mining only