CLEC18A

protein-coding

C-type lectin domain family 18 member A, the group of CAP and C-type lectin domain containing|C-type lectin domain containing

Gene summary

This is one of three closely related paralogous genes on chromosome 16 encoding secreted proteins containing C-type lectin domains. These domains bind to carbohydrates in the presence of calcium, and may be involved in cell adhesion, immune response and apoptosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2012]

Previous symbols:

MRCL

MANE transcript

NM_001370523.4

Inheritance

—

ClinVar variants

U:64B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr16:69,950,705-69,964,452

External References & Databases

Ensembl (ENSG00000157322)

Transcript & Mutation Effects

hg38 • Region Span ~13.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLEC18A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 66

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370523.4. 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						0
missense			64 clinvar	2 clinvar		66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	2	0	66

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370523.4	RefSeq	NP_001357452.1	12	MANE Select
ENST00000288040.11	Ensembl	ENSP00000288040.6	12	MANE Select
NM_001136214.4	RefSeq	NP_001129686.1	12	Standard
NM_001271197.3	RefSeq	NP_001258126.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
polysaccharide binding

Cellular Component

extracellular space
endosome
endoplasmic reticulum
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000288040
Coding exons: 12
Length: 13332
Individuals with no LoFs: 124695
Homozygous LoFs: 3
Heterozygous LoFs: 15
Defined: 124713
p: 0.0000722

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.190	74	78.7	0.940	0.00000493	2868
Missense (PolyPhen)		17	22.253	0.76393		1181
Synonymous	-0.565	36	31.9	1.13	0.00000213	837
Loss of Function	0.992	4	6.79	0.589	2.92e-7	272

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00012	rare
South Asian	0.00010	0.000065	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds polysaccharides in a Ca(2+)-independent manner with a preferentially binding to fucoidan, beta-glucans and galactans (PubMed:26170455). {ECO:0000269|PubMed:26170455}.;

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.146

Gene Damage Prediction

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