COLEC12

collectin subfamily member 12, the group of C-type lectin domain containing|Collectins|Scavenger receptors

Basic information

Region (hg38): 18:316737-500722

Links

ENSG00000158270

∙ NCBI:81035 ∙ OMIM:607621 ∙ HGNC:16016 ∙ Uniprot:Q5KU26 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COLEC12 gene.

not_specified (84 variants)
not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COLEC12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000130386.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			79 clinvar	5 clinvar	1 clinvar	85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	7	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COLEC12	protein_coding	protein_coding	ENST00000400256	10	181362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.908	0.0924	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	318	402	0.791	0.0000220	4854
Missense in Polyphen		61	77.008	0.79212		1035
Synonymous	-0.381	168	162	1.04	0.00000955	1433
Loss of Function	4.20	5	29.7	0.168	0.00000135	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000727	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000690	0.0000653
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid-beta in Alzheimer disease. {ECO:0000269|PubMed:11162630, ECO:0000269|PubMed:11564734, ECO:0000269|PubMed:12761161, ECO:0000269|PubMed:15845541, ECO:0000269|PubMed:16868960}.;
Pathway: Phagosome - Homo sapiens (human);Vesicle-mediated transport;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors (Consensus)

Recessive Scores

pRec: 0.180

Intolerance Scores

loftool: 0.0353
rvis_EVS: 1.34
rvis_percentile_EVS: 94.25

Haploinsufficiency Scores

pHI: 0.279
hipred: Y
hipred_score: 0.640
ghis: 0.462

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Colec12
Phenotype

Zebrafish Information Network

Gene name: colec12
Affected structure: intersegmental vessel
Phenotype tag: abnormal
Phenotype quality: aplastic

Gene ontology

Biological process: receptor-mediated endocytosis;phagocytosis, recognition;defense response;carbohydrate mediated signaling;toll-like receptor 3 signaling pathway;innate immune response;regulation of immune response;protein homooligomerization;positive regulation of cell adhesion molecule production;cellular response to exogenous dsRNA
Cellular component: collagen trimer;extracellular space;plasma membrane;integral component of membrane;endocytic vesicle membrane;extracellular matrix
Molecular function: scavenger receptor activity;galactose binding;signaling pattern recognition receptor activity;low-density lipoprotein particle binding;metal ion binding