COLEC12

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

Basic information

Region (hg38): 18:316736-500722

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.

• Inborn genetic diseases (22 variants)
• not provided (7 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.

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				1	1	2
missense			20	3	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					2	2
Total	0	0	20	4	4

Variants in COLEC12

This is a list of pathogenic ClinVar variants found in the COLEC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-321680-C-T		not specified	Uncertain significance (Dec 13, 2022)
18-321698-C-T		not specified	Likely benign (May 08, 2023)
18-321766-T-C		not specified	Uncertain significance (Feb 06, 2023)
18-321773-G-A		not specified	Uncertain significance (Feb 15, 2023)
18-331713-C-T		not specified	Likely benign (Jul 17, 2023)
18-333047-T-A		not specified	Uncertain significance (Aug 21, 2023)
18-333137-G-A		not specified	Uncertain significance (Dec 15, 2022)
18-334758-T-T			Benign (Dec 31, 2019)
18-334759-G-A		not specified	Uncertain significance (Aug 02, 2021)
18-334795-G-A		not specified	Uncertain significance (Jan 26, 2023)
18-334803-T-C			Benign (Jun 19, 2018)
18-334870-C-T		not specified	Uncertain significance (Jan 02, 2024)
18-334966-G-T		not specified	Uncertain significance (Jan 19, 2024)
18-334972-G-C		not specified	Uncertain significance (Jan 19, 2024)
18-334994-A-A			Benign (Dec 31, 2019)
18-335057-A-G		not specified	Uncertain significance (Jul 25, 2023)
18-335075-C-G		not specified	Uncertain significance (Aug 16, 2022)
18-335093-G-A		not specified	Uncertain significance (Jan 22, 2024)
18-335116-G-A		not specified	Uncertain significance (Apr 19, 2023)
18-346444-C-T		not specified	Uncertain significance (Sep 15, 2021)
18-346549-C-G		not specified	Uncertain significance (Sep 13, 2023)
18-346549-C-T		not specified	Uncertain significance (Sep 01, 2021)
18-346585-A-T		not specified	Uncertain significance (Dec 20, 2023)
18-346663-T-A		not specified	Uncertain significance (Jan 09, 2024)
18-346679-G-T		not specified	Uncertain significance (Feb 05, 2024)

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

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