CLEC1A C-type lectin domain family 1 member A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLEC1Aprovided by HGNC
Official Full Name: C-type lectin domain family 1 member Aprovided by HGNC
Primary source: HGNC:HGNC:24355
See related: Ensembl:ENSG00000150048 MIM:606782; AllianceGenome:HGNC:24355
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CLEC1; CLEC-1
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]
Expression: Biased expression in placenta (RPKM 18.1), lung (RPKM 3.8) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (10069554..10098985, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (9955966..9985656, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (10222153..10251584, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CLEC-1 Acts as a Negative Regulator of Dectin-1 Induced Host Inflammatory Response Signature in Aspergillus fumigatus Keratitis.
Title: CLEC-1 Acts as a Negative Regulator of Dectin-1 Induced Host Inflammatory Response Signature in Aspergillus fumigatus Keratitis.
Histidine-Rich Glycoprotein Stimulates Human Neutrophil Phagocytosis and Prolongs Survival through CLEC1A.
Title: Histidine-Rich Glycoprotein Stimulates Human Neutrophil Phagocytosis and Prolongs Survival through CLEC1A.
Expression of CLEC-1 mRNA was detected in myeloid cells as well as in endothelial cells. CLEC-1 protein displayed N-linked glycosylation and formed dimers.
Title: The human C-type lectin-like receptor CLEC-1 is upregulated by TGF-β and primarily localized in the endoplasmic membrane compartment.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Aspergillosis, susceptibility to MedGen: C3279774 OMIM: 614079 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A009U38 (e-PCR)
- UniSTS:83033

G32855 (e-PCR)
- UniSTS:117434

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane signaling receptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cell surface receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: C-type lectin domain family 1 member A

Names: C-type lectin-like receptor-1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001297748.2 → NP_001284677.1 C-type lectin domain family 1 member A isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AC024224, AK091989, BC067746

Consensus CDS

CCDS73443.1

UniProtKB/TrEMBL

B3KRP6, E9PFB4

Related

ENSP00000415048.2, ENST00000457018.6

Conserved Domains (1) summary

cd03593
Location:104 → 226

CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
NM_001297749.2 → NP_001284678.1 C-type lectin domain family 1 member A isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two alternate in-frame exons in the 5' coding region compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC024224, AK300979, AY358587, BC067746

Consensus CDS

CCDS76528.1

UniProtKB/TrEMBL

B4DV89, E7ESV9

Related

ENSP00000417010.2, ENST00000420265.2

Conserved Domains (1) summary

cd03593
Location:45 → 167

CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
NM_001297750.2 → NP_001284679.1 C-type lectin domain family 1 member A isoform d

See identical proteins and their annotated locations for NP_001284679.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate exon compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG to encode an isoform (d) that has a shorter N-terminus, compared to isoform a. Variants 4 and 5 encode the same isoform.

Source sequence(s)

AC024224, AY358587, BC067746, BX380212

UniProtKB/TrEMBL

B4DV89

Conserved Domains (1) summary

cd03593
Location:49 → 171

CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
NM_001297751.2 → NP_001284680.1 C-type lectin domain family 1 member A isoform d

See identical proteins and their annotated locations for NP_001284680.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG to encode an isoform (d) that has a shorter N-terminus, compared to isoform a. Variants 4 and 5 encode the same isoform.

Source sequence(s)

AC024224, AY358587, BC067746, BX339075

UniProtKB/TrEMBL

B4DV89

Conserved Domains (1) summary

cd03593
Location:49 → 171

CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
NM_016511.4 → NP_057595.2 C-type lectin domain family 1 member A isoform a

See identical proteins and their annotated locations for NP_057595.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AC024224, AK075114, BC067746

Consensus CDS

CCDS8612.1

UniProtKB/Swiss-Prot

Q8IUW7, Q8NC01, Q9NZH3

UniProtKB/TrEMBL

A8K6B9

Related

ENSP00000326407.4, ENST00000315330.8

Conserved Domains (1) summary

cd03593
Location:137 → 259

CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

10069554..10098985 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011520687.3 → XP_011518989.1 C-type lectin domain family 1 member A isoform X1

UniProtKB/TrEMBL

A8K6B9

Conserved Domains (1) summary

cd03593
Location:164 → 286

CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)