CLEC9A

C-type lectin domain containing 9A, the group of C-type lectin domain containing|CD molecules

Basic information

Region (hg38): 12:10030678-10066031

Links

ENSG00000197992 ∙ NCBI:283420 ∙ OMIM:612252 ∙ HGNC:26705 ∙ Uniprot:Q6UXN8 ∙ 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 CLEC9A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC9A gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			11	4	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	4	1

Variants in CLEC9A

This is a list of pathogenic ClinVar variants found in the CLEC9A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-10052733-G-A			Benign (Jul 04, 2018)
12-10054271-G-A		not specified	Uncertain significance (Jun 09, 2022)
12-10054294-A-G		not specified	Uncertain significance (Apr 11, 2023)
12-10054312-A-G		not specified	Likely benign (Nov 13, 2023)
12-10061145-T-C		not specified	Uncertain significance (Dec 13, 2022)
12-10061148-C-T		not specified	Uncertain significance (Jul 05, 2022)
12-10061163-A-C		not specified	Uncertain significance (Mar 05, 2024)
12-10061179-A-C		not specified	Uncertain significance (Jun 13, 2022)
12-10061216-A-C		not specified	Uncertain significance (Jan 26, 2022)
12-10061232-T-A		not specified	Uncertain significance (Nov 30, 2022)
12-10061249-T-C		not specified	Likely benign (Jul 28, 2021)
12-10063070-C-G		not specified	Uncertain significance (Feb 13, 2024)
12-10063100-A-G		not specified	Uncertain significance (Jul 05, 2023)
12-10064813-C-T		not specified	Uncertain significance (Jun 21, 2021)
12-10064850-G-A		not specified	Likely benign (Apr 12, 2023)
12-10065510-G-C		not specified	Likely benign (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC9A	protein_coding	protein_coding	ENST00000355819	6	35290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000185	0.708	125656	0	86	125742	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.504	110	126	0.874	0.00000630	1591
Missense in Polyphen		17	27.557	0.61691		416
Synonymous	-0.742	54	47.5	1.14	0.00000286	401
Loss of Function	1.03	9	13.0	0.691	5.52e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00435	0.00434
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000239	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an endocytic receptor on a small subset of myeloid cells specialized for the uptake and processing of material from dead cells. Recognizes filamentous form of actin in association with particular actin-binding domains of cytoskeletal proteins, including spectrin, exposed when cell membranes are damaged, and mediate the cross-presentation of dead-cell associated antigens in a Syk-dependent manner. {ECO:0000269|PubMed:18497879, ECO:0000269|PubMed:22483802}.

Recessive Scores

• pRec: 0.0765

Intolerance Scores

• loftool: 0.785
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.21

Haploinsufficiency Scores

• pHI: 0.0714
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.117

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec9a
• Phenotype: immune system phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis;positive regulation of cytokine secretion
• Cellular component: cell surface;integral component of membrane
• Molecular function: carbohydrate binding