COLEC11

collectin subfamily member 11, the group of C-type lectin domain containing|Complement system activation components|Collectins

Basic information

Region (hg38): 2:3594831-3644644

Links

ENSG00000118004 ∙ NCBI:78989 ∙ OMIM:612502 ∙ HGNC:17213 ∙ Uniprot:Q9BWP8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 3MC syndrome (Supportive), mode of inheritance: AR
• 3MC syndrome 2 (Definitive), mode of inheritance: AR
• 3MC syndrome 2 (Strong), mode of inheritance: AR
• 3MC syndrome 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
3MC syndrome 2	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal	2569826; 8933348; 21258343

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COLEC11 gene.

• not provided (41 variants)
• Inborn genetic diseases (17 variants)
• 3MC syndrome 2 (8 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COLEC11 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				10	6	16
missense	1		24	7	1	33
nonsense						0
start loss						0
frameshift	1	1	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding			1	4	4	9
Total	2	1	26	21	11

Highest pathogenic variant AF is 0.000118

Variants in COLEC11

This is a list of pathogenic ClinVar variants found in the COLEC11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-3603614-G-C		not specified	Uncertain significance (Sep 28, 2016)
2-3603636-G-A		COLEC11-related disorder	Likely benign (Aug 23, 2019)
2-3603645-G-A		COLEC11-related disorder	Likely benign (Apr 19, 2023)
2-3603669-C-T		COLEC11-related disorder	Likely benign (Mar 20, 2019)
2-3603670-G-A		COLEC11-related disorder	Likely benign (Apr 29, 2020)
2-3604310-T-C		COLEC11-related disorder	Likely benign (May 05, 2020)
2-3604350-A-C		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
2-3604351-A-G		Inborn genetic diseases	Uncertain significance (Oct 14, 2021)
2-3604363-T-C			Benign/Likely benign (Jan 23, 2024)
2-3604366-G-T		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
2-3604368-G-T		3MC syndrome 2	Uncertain significance (Mar 30, 2021)
2-3604383-GC-G		3MC syndrome 2	Pathogenic (Mar 01, 2011)
2-3604419-CCGGCTGGCGATGA-C		3MC syndrome	Pathogenic (Jul 07, 2023)
2-3604434-G-A		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
2-3604451-C-T		Inborn genetic diseases	Likely benign (Sep 20, 2023)
2-3604454-C-T		COLEC11-related disorder	Uncertain significance (Nov 01, 2023)
2-3604476-C-T		COLEC11-related disorder	Likely benign (Sep 29, 2020)
2-3604485-G-A			Likely benign (Aug 20, 2022)
2-3606186-T-C		COLEC11-related disorder	Likely benign (Mar 02, 2021)
2-3606210-A-T		COLEC11-related disorder	Uncertain significance (Jan 11, 2024)
2-3606254-T-C		not specified	Benign (Mar 28, 2016)
2-3613308-C-T		not specified	Uncertain significance (Feb 04, 2024)
2-3613317-C-T			Uncertain significance (Aug 06, 2022)
2-3613342-C-T			Likely benign (May 12, 2023)
2-3613345-C-T		Inborn genetic diseases	Likely benign (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COLEC11	protein_coding	protein_coding	ENST00000418971	7	49623

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0175	0.963	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.564	159	180	0.882	0.0000131	1844
Missense in Polyphen		60	84.026	0.71406		814
Synonymous	-0.903	87	76.9	1.13	0.00000668	563
Loss of Function	2.04	5	12.9	0.388	5.62e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000398
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000652	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lectin that plays a role in innate immunity, apoptosis and embryogenesis (PubMed:23954398, PubMed:25912189, PubMed:21258343). Calcium-dependent lectin that binds self and non-self glycoproteins presenting high mannose oligosaccharides with at least one terminal alpha-1,2-linked mannose epitope (PubMed:25912189). Primarily recognizes the terminal disaccharide of the glycan (PubMed:25912189). Also recognizes a subset of fucosylated glycans and lipopolysaccharides (PubMed:17179669, PubMed:25912189). Plays a role in innate immunity through its ability to bind non-self sugars presented by microorganisms and to activate the complement through the recruitment of MAPS1 (PubMed:20956340, PubMed:25912189). Also plays a role in apoptosis through its ability to bind in a calcium-independent manner the DNA present at the surface of apoptotic cells and to activate the complement in response to this binding (Probable). Finally, plays a role in development, probably serving as a guidance cue during the migration of neural crest cells and other cell types during embryogenesis (PubMed:21258343, PubMed:28301481). {ECO:0000269|PubMed:17179669, ECO:0000269|PubMed:20956340, ECO:0000269|PubMed:21258343, ECO:0000269|PubMed:23954398, ECO:0000269|PubMed:25912189, ECO:0000269|PubMed:28301481, ECO:0000305|PubMed:20956340, ECO:0000305|PubMed:23954398}.
• Pathway: Phagosome - Homo sapiens (human);Vitamin D Receptor Pathway;Vesicle-mediated transport;Innate Immune System;Immune System;Initial triggering of complement;Lectin pathway of complement activation;Creation of C4 and C2 activators;Complement cascade;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.322
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.502
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.267

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Colec11
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: colec11
• Affected structure: neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: complement activation, lectin pathway;proteolysis;receptor-mediated endocytosis;complement activation;multicellular organism development;antimicrobial humoral response;developmental process;execution phase of apoptosis
• Cellular component: extracellular region;collagen trimer;extracellular space
• Molecular function: DNA binding;serine-type endopeptidase activity;calcium ion binding;protein binding;mannose binding;fucose binding;monosaccharide binding;oligosaccharide binding;calcium-dependent carbohydrate binding