CLEC5A

protein-coding

C-type lectin domain containing 5A, 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 signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type II transmembrane protein interacts with dnax-activation protein 12 and may play a role in cell activation. Alternative splice variants have been described but their full-length sequence has not been determined. [provided by RefSeq, Jul 2008]

Previous symbols:

CLECSF5

MANE transcript

NM_013252.3

Inheritance

—

ClinVar variants

U:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr7:141,927,357-141,947,007

External References & Databases

Ensembl (ENSG00000258227)

Transcript & Mutation Effects

hg38 • Region Span ~19.7 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 CLEC5A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 25

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013252.3. 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			25 clinvar			25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	0	0	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013252.3	RefSeq	NP_037384.1	6	MANE Select
ENST00000546910.6	Ensembl	ENSP00000449999.1	6	MANE Select
NM_001301167.2	RefSeq	NP_001288096.1	5	Standard
ENST00000418498.5	Ensembl	ENSP00000392561.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
DAP12 interactions
Innate Immune System
Immune System

Biological Process

osteoblast development
cellular defense response
signal transduction
myeloid cell differentiation
negative regulation of myeloid cell apoptotic process

Molecular Function

virus receptor activity
protein binding
carbohydrate binding

Cellular Component

cytosol
plasma membrane
integral component of plasma membrane
cell surface
specific granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000546910
Coding exons: 6
Length: 19651
Individuals with no LoFs: 125578
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125579
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.236	94	101	0.934	0.00000500	1255
Missense (PolyPhen)		19	25.623	0.74151		328
Synonymous	0.193	32	33.4	0.957	0.00000178	315
Loss of Function	1.99	3	9.66	0.311	4.07e-7	120

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
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)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions as a positive regulator of osteoclastogenesis (By similarity). Cell surface receptor that signals via TYROBP (PubMed:10449773). Regulates inflammatory responses (By similarity). {ECO:0000250|UniProtKB:Q9R007, ECO:0000269|PubMed:10449773}.;

Recessive Scores

pRec: 0.0948

Intolerance Scores

LoFtool: 0.600
RVIS EVS: 0.22
RVIS percentile EVS: 67.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.137

Gene Damage Prediction

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