CD300A

CD300a molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 17:74466399-74484798

Links

ENSG00000167851 ∙ NCBI:11314 ∙ OMIM:606790 ∙ HGNC:19319 ∙ Uniprot:Q9UGN4 ∙ 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 CD300A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD300A 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	16	2	0

Variants in CD300A

This is a list of pathogenic ClinVar variants found in the CD300A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74466709-G-C		not specified	Uncertain significance (Apr 16, 2024)
17-74466711-T-A		not specified	Uncertain significance (Mar 29, 2023)
17-74466718-G-T		not specified	Uncertain significance (Jan 29, 2024)
17-74466719-G-A		not specified	Uncertain significance (May 30, 2023)
17-74466740-C-G		not specified	Uncertain significance (May 13, 2024)
17-74473547-C-G		not specified	Uncertain significance (Jan 11, 2023)
17-74473565-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-74473583-G-A		not specified	Uncertain significance (Jun 13, 2023)
17-74473684-G-C		not specified	Uncertain significance (Nov 07, 2022)
17-74473788-C-G		not specified	Uncertain significance (Mar 21, 2022)
17-74473818-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-74473872-C-A		not specified	Uncertain significance (Mar 16, 2022)
17-74474559-T-C		not specified	Uncertain significance (Oct 16, 2023)
17-74474586-C-G		not specified	Uncertain significance (Jan 26, 2023)
17-74474671-G-T		not specified	Uncertain significance (May 08, 2024)
17-74477509-A-G		not specified	Uncertain significance (May 25, 2022)
17-74481816-G-T		not specified	Uncertain significance (Mar 28, 2024)
17-74484010-A-G		not specified	Uncertain significance (Jan 02, 2024)
17-74484022-C-T		not specified	Uncertain significance (Jan 30, 2024)
17-74484061-A-T		not specified	Uncertain significance (Jun 14, 2022)
17-74484080-G-A		not specified	Likely benign (Feb 08, 2023)
17-74484085-G-A		not specified	Likely benign (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD300A	protein_coding	protein_coding	ENST00000360141	7	18379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000115	0.589	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.229	157	165	0.950	0.00000850	1910
Missense in Polyphen		39	41.427	0.94142		525
Synonymous	0.494	66	71.3	0.926	0.00000425	615
Loss of Function	0.939	11	14.9	0.738	7.20e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000110	0.000109
South Asian	0.0000368	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitory receptor which may contribute to the down- regulation of cytolytic activity in natural killer (NK) cells, and to the down-regulation of mast cell degranulation (PubMed:10746781, PubMed:16339535, PubMed:9701027). Negatively regulates the Toll-like receptor (TLR) signaling mediated by MYD88 but not TRIF through activation of PTPN6 (PubMed:22043923). {ECO:0000269|PubMed:10746781, ECO:0000269|PubMed:16339535, ECO:0000269|PubMed:22043923, ECO:0000269|PubMed:9701027}.
• Pathway: Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.854
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.283
• hipred: N
• hipred_score: 0.112
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00480

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd300a
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: cell adhesion;negative regulation of B cell proliferation;positive regulation of phosphoprotein phosphatase activity;negative regulation of mast cell activation involved in immune response;negative regulation of MyD88-dependent toll-like receptor signaling pathway;negative regulation of mast cell degranulation;neutrophil degranulation;negative regulation of MAP kinase activity;negative regulation of fibroblast proliferation;regulation of immune response;regulation of T cell receptor signaling pathway;negative regulation of B cell receptor signaling pathway;negative regulation of NK T cell activation;negative regulation of phagocytosis, engulfment;negative regulation of neutrophil activation;negative regulation of eosinophil activation;negative regulation of activation of Janus kinase activity;negative regulation of eosinophil migration
• Cellular component: plasma membrane;membrane;integral component of membrane;extracellular exosome;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: phosphatidylserine binding;protein binding;phosphatidylethanolamine binding;signaling receptor activity