COLEC10

protein-coding

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

Gene summary

This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006438.5

Inheritance

ClinVar variants

P:6U:44B:10

Top phenotype

3MC syndrome 3

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr8:118,995,452-119,108,455

External References & Databases

Ensembl (ENSG00000184374)

Transcript & Mutation Effects

hg38 • Region Span ~113.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

3MC syndrome 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009554

Submitter: G2P

3MC syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0017398

Submitter: Orphanet

Clinical Genomic Database (CGD)

3MC syndrome 3AR

Manifestation: Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal

Intervention: General

Rationale: 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

Refs: 28301481

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COLEC10 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 10

3MC syndrome 3Total: 7

COLEC10-related disorderTotal: 5

Primary immunodeficiency or monogenic inflammatory bowel diseaseTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006438.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	1 clinvar	6
missense	1 clinvar	1 clinvar	44 clinvar	4 clinvar		50
nonsense	1 clinvar					1
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	4	2	44	9	1	60

Highest pathogenic variant AF is 0.00011444722

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006438.5	RefSeq	NP_006429.2	6	MANE Select
ENST00000332843.3	Ensembl	ENSP00000332723.2	6	MANE Select
NM_001324095.2	RefSeq	NP_001311024.1	5	Standard
ENST00000892374.1	Ensembl	ENSP00000562433.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Innate Immune System
Immune System
Initial triggering of complement
Lectin pathway of complement activation
Creation of C4 and C2 activators

Biological Process

complement activation, lectin pathway
proteolysis
complement activation
developmental process
positive chemotaxis

Molecular Function

serine-type endopeptidase activity
mannose binding
chemoattractant activity
monosaccharide binding

Cellular Component

extracellular region
collagen trimer
extracellular space
cytoplasm
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000332843
Coding exons: 6
Length: 111131
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125735
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0281	158	159	0.994	0.00000836	1831
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.00056	0.00056	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.138

Intolerance Scores

LoFtool: 0.320
RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.323

Gene Damage Prediction

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