CD300LF

CD300 molecule like family member f, the group of V-set domain containing

Basic information

Region (hg38): 17:74694310-74712978

Links

ENSG00000186074 ∙ NCBI:146722 ∙ OMIM:609807 ∙ HGNC:29883 ∙ Uniprot:Q8TDQ1 ∙ 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 CD300LF gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD300LF 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				1		1
missense			11	1		12
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	2	0

Variants in CD300LF

This is a list of pathogenic ClinVar variants found in the CD300LF region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74695146-C-T		not specified	Likely benign (Dec 23, 2022)
17-74695151-A-G		not specified	Uncertain significance (Mar 01, 2023)
17-74695223-T-C		not specified	Uncertain significance (Sep 15, 2021)
17-74695777-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-74695838-C-T		not specified	Uncertain significance (Aug 09, 2021)
17-74698468-T-G		not specified	Uncertain significance (Dec 05, 2022)
17-74698475-C-G		not specified	Likely benign (Nov 22, 2023)
17-74698480-G-A		not specified	Uncertain significance (Sep 22, 2023)
17-74703054-C-T		not specified	Likely benign (Oct 17, 2023)
17-74704537-C-T		not specified	Uncertain significance (Dec 13, 2023)
17-74704590-C-A			Likely benign (Mar 01, 2023)
17-74704591-G-A		not specified	Uncertain significance (May 16, 2022)
17-74704624-C-G		not specified	Uncertain significance (Jan 26, 2022)
17-74704688-T-G		not specified	Uncertain significance (Sep 27, 2021)
17-74704696-C-T		not specified	Uncertain significance (Jan 08, 2024)
17-74704729-G-A		not specified	Uncertain significance (Jan 11, 2023)
17-74704750-G-A		not specified	Uncertain significance (Sep 01, 2021)
17-74704787-G-A		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD300LF	protein_coding	protein_coding	ENST00000326165	7	18666

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-8	0.182	125708	0	36	125744	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.358	150	163	0.921	0.00000891	1860
Missense in Polyphen		32	34.405	0.93009		446
Synonymous	-0.584	75	68.8	1.09	0.00000408	584
Loss of Function	0.322	13	14.3	0.908	6.81e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000925	0.000925
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an inhibitory receptor for myeloid cells and mast cells (PubMed:15549731). Positively regulates the phagocytosis of apoptotic cells (efferocytosis) via phosphatidylserine (PS) recognition; recognizes and binds PS as a ligand which is expressed on the surface of apoptotic cells. Plays an important role in the maintenance of immune homeostasis, by promoting macrophage-mediated efferocytosis and by inhibiting dendritic cell-mediated efferocytosis (By similarity). Negatively regulates Fc epsilon receptor-dependent mast cell activation and allergic responses via binding to ceramide and sphingomyelin which act as ligands (PubMed:24035150). May act as a coreceptor for interleukin 4 (IL-4). Associates with and regulates IL-4 receptor alpha-mediated responses by augmenting IL-4- and IL-13-induced signaling (By similarity). Negatively regulates the Toll-like receptor (TLR) signaling mediated by MYD88 and TRIF through activation of PTPN6/SHP-1 and PTPN11/SHP-2 (PubMed:22043923). Inhibits osteoclast formation. Induces macrophage cell death upon engagement (By similarity). {ECO:0000250|UniProtKB:Q6SJQ7, ECO:0000269|PubMed:15549731, ECO:0000269|PubMed:22043923, ECO:0000269|PubMed:24035150}.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.780
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.0337
• hipred: N
• hipred_score: 0.178
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00234

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd300lf
• Phenotype: respiratory system phenotype; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of mast cell activation;negative regulation of MyD88-dependent toll-like receptor signaling pathway;TRIF-dependent toll-like receptor signaling pathway;interleukin-13-mediated signaling pathway;regulation of immune response;positive regulation of interleukin-4-mediated signaling pathway;negative regulation of apoptotic cell clearance;positive regulation of apoptotic cell clearance
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: phosphatidylserine binding;interleukin-4 receptor binding;ceramide binding