CLEC5A

C-type lectin domain containing 5A, the group of C-type lectin domain containing

Basic information

Region (hg38): 7:141927357-141947007

Previous symbols: [ "CLECSF5" ]

Links

ENSG00000258227

∙ NCBI:23601 ∙ OMIM:604987 ∙ HGNC:2054 ∙ Uniprot:Q9NY25 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLEC5A gene.

not_specified (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC5A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013252.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC5A	protein_coding	protein_coding	ENST00000546910	6	19651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.126	0.853	125578	0	1	125579	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.236	94	101	0.934	0.00000500	1255
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.;
Pathway: Neutrophil degranulation;DAP12 interactions;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec: 0.0948

Intolerance Scores

loftool: 0.600
rvis_EVS: 0.22
rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

pHI: 0.0997
hipred: N
hipred_score: 0.172
ghis: 0.416

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Clec5a
Phenotype: skeleton phenotype; immune system phenotype;

Gene ontology

Biological process: osteoblast development;cellular defense response;signal transduction;myeloid cell differentiation;negative regulation of myeloid cell apoptotic process;negative regulation of apoptotic process;neutrophil degranulation;innate immune response;viral entry into host cell;positive regulation of cytokine secretion
Cellular component: cytosol;plasma membrane;integral component of plasma membrane;cell surface;specific granule membrane;tertiary granule membrane
Molecular function: virus receptor activity;protein binding;carbohydrate binding