CLEC1A

protein-coding

C-type lectin domain family 1 member A, the group of C-type lectin domain containing

Gene summary

This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The encoded protein may play a role in regulating dendritic cell function. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

MANE transcript

NM_016511.4

Inheritance

—

ClinVar variants

U:32B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.55

Max pathogenic AF

—

Genomic locus

chr12:10,069,554-10,111,627

External References & Databases

Ensembl (ENSG00000150048)

Transcript & Mutation Effects

hg38 • Region Span ~42.1 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 CLEC1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016511.4. 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			32 clinvar	9 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	9	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016511.4	RefSeq	NP_057595.2	6	MANE Select
ENST00000315330.8	Ensembl	ENSP00000326407.4	6	MANE Select
NM_001297748.2	RefSeq	NP_001284677.1	5	Standard
NM_001297749.2	RefSeq	NP_001284678.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

defense response
cell surface receptor signaling pathway

Molecular Function

transmembrane signaling receptor activity
carbohydrate binding

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000315330
Coding exons: 6
Length: 42074
Individuals with no LoFs: 125584
Homozygous LoFs: 1
Heterozygous LoFs: 163
Defined: 125748
p: 0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.151	155	150	1.03	0.00000773	1839
Missense (PolyPhen)		23	23.338	0.98552		317
Synonymous	0.593	50	55.6	0.899	0.00000285	512
Loss of Function	-1.86	21	13.6	1.55	6.61e-7	154

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00035	0.00032	rare
Ashkenazi Jewish	0.0076	0.0077	notable
East Asian	0.00082	0.00082	rare
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00037	0.00035	rare
South Asian	0.00033	0.00033	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0754

Intolerance Scores

LoFtool: 0.848
RVIS EVS: 0.53
RVIS percentile EVS: 80.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0462

Gene Damage Prediction

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