COLEC10

collectin subfamily member 10, the group of C-type lectin domain containing|Complement system activation components|Collectins

Basic information

Region (hg38): 8:118995452-119108455

Links

ENSG00000184374 ∙ NCBI:10584 ∙ OMIM:607620 ∙ HGNC:2220 ∙ Uniprot:Q9Y6Z7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
3MC syndrome 3	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal	28301481

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COLEC10 gene.

• 3MC syndrome 3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COLEC10 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				3	2	5
missense			12	2		14
nonsense		1				1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	1	1	13	5	2

Highest pathogenic variant AF is 0.00000658

Variants in COLEC10

This is a list of pathogenic ClinVar variants found in the COLEC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-119067306-C-T		3MC syndrome 3 • See cases • COLEC10-related disorder	Pathogenic (Nov 07, 2019)
8-119067330-G-C		not specified	Likely benign (Jun 07, 2024)
8-119067343-T-G		not specified	Uncertain significance (Nov 08, 2024)
8-119067348-A-G		not specified	Uncertain significance (Jul 30, 2024)
8-119067354-A-G		not specified	Uncertain significance (May 08, 2023)
8-119067387-G-A		not specified	Likely benign (Jul 06, 2021)
8-119067391-A-C		not specified	Uncertain significance (Nov 29, 2023)
8-119067400-CCA-C		3MC syndrome 3	Pathogenic (Jan 01, 2020)
8-119067402-A-G		not specified	Uncertain significance (Sep 22, 2023)
8-119081735-A-C			Uncertain significance (Jun 10, 2021)
8-119089737-G-C		not specified	Uncertain significance (Jun 26, 2024)
8-119089747-G-A			Benign (Dec 31, 2019)
8-119091153-TA-T		3MC syndrome 3	Pathogenic (Apr 13, 2017)
8-119091205-C-T		not specified	Uncertain significance (Jun 05, 2024)
8-119091214-A-G		not specified	Uncertain significance (Nov 21, 2023)
8-119102363-A-G		not specified	Uncertain significance (Jun 03, 2024)
8-119102365-G-A		3MC syndrome 3	Uncertain significance (Mar 26, 2024)
8-119102366-G-C		not specified	Uncertain significance (Sep 11, 2024)
8-119102379-A-G		not specified	Uncertain significance (Oct 10, 2023)
8-119102381-C-G		not specified	Uncertain significance (Feb 12, 2024)
8-119102406-G-A			Benign (Dec 31, 2019)
8-119103808-T-A		not specified	Uncertain significance (Jan 30, 2024)
8-119103825-C-T			Likely benign (Sep 01, 2024)
8-119103843-A-G		COLEC10-related disorder	Benign (Mar 08, 2019)
8-119103863-G-A		not specified	Uncertain significance (Apr 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COLEC10	protein_coding	protein_coding	ENST00000332843	6	111131

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00262	0.940	125708	0	27	125735	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0281	158	159	0.994	0.00000836	1831
Missense in Polyphen		64	73.217	0.87411		847
Synonymous	0.713	47	53.6	0.876	0.00000270	510
Loss of Function	1.66	6	12.3	0.489	5.82e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000878	0.0000878
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.000556	0.000555
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lectin that binds to various sugars: galactose > mannose = fucose > N-acetylglucosamine > N-acetylgalactosamine (PubMed:10224141). Acts as a chemoattractant, probably involved in the regulation of cell migration (PubMed:28301481). {ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}.
• Pathway: Innate Immune System;Immune System;Initial triggering of complement;Lectin pathway of complement activation;Creation of C4 and C2 activators;Complement cascade (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.320
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.270
• hipred: N
• hipred_score: 0.496
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.323

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Colec10

Gene ontology

• Biological process: complement activation, lectin pathway;proteolysis;complement activation;developmental process;positive chemotaxis;cranial skeletal system development
• Cellular component: extracellular region;collagen trimer;extracellular space;cytoplasm;Golgi apparatus
• Molecular function: serine-type endopeptidase activity;mannose binding;chemoattractant activity;monosaccharide binding