GeneBe

COLEC11

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

Basic information

Region (hg38): 2:3594832-3644644

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
3MC syndrome 2ARAudiologic/OtolaryngologicEarly recognition and treatment of hearing impairment may improve outcomes, including speech and language developmentAudiologic/Otolaryngologic; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal2569826; 8933348; 21258343

ClinVar

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

  • not_provided (50 variants)
  • Inborn_genetic_diseases (39 variants)
  • COLEC11-related_disorder (23 variants)
  • 3MC_syndrome_2 (14 variants)
  • not_specified (3 variants)
  • 3MC_syndrome (1 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. These statistics are base on transcript: NM_000024027.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
26
clinvar
4
clinvar
 31
missense
2
clinvar
44
clinvar
6
clinvar
 52
nonsense
0
start loss
0
frameshift
2
clinvar
2
clinvar
1
clinvar
 5
splice donor/acceptor (+/-2bp)
0
Total 4 2 46 32 4

Highest pathogenic variant AF is 0.000016727588

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
COLEC11protein_codingprotein_codingENST00000418971 749623
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.01750.9631257300181257480.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5641591800.8820.00001311844
Missense in Polyphen6084.0260.71406814
Synonymous-0.9038776.91.130.00000668563
Loss of Function2.04512.90.3885.62e-7157

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003980.000398
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00006520.0000615
Middle Eastern0.0001090.000109
South Asian0.00006530.0000327
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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