CD69

CD69 molecule, the group of CD molecules|C-type lectin domain containing

Basic information

Region (hg38): 12:9752486-9760901

Links

ENSG00000110848 ∙ NCBI:969 ∙ OMIM:107273 ∙ HGNC:1694 ∙ Uniprot:Q07108 ∙ 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 CD69 gene.

• not_specified (14 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD69 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001781.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			11	3		14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	11	3	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD69	protein_coding	protein_coding	ENST00000228434	5	8416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0297	0.929	124493	0	2	124495	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.259	112	105	1.07	0.00000502	1322
Missense in Polyphen		16	25.393	0.6301		341
Synonymous	1.05	28	36.0	0.777	0.00000180	349
Loss of Function	1.75	4	9.98	0.401	5.21e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets.
• Pathway: IL-3 Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.396

Intolerance Scores

• loftool: 0.724
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.112
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.513

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd69
• Phenotype: cellular phenotype; immune system phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cellular response to drug
• Cellular component: integral component of plasma membrane;external side of plasma membrane;protein-containing complex
• Molecular function: transmembrane signaling receptor activity;calcium ion binding;protein binding;carbohydrate binding;protein homodimerization activity