CD300LF

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

Basic information

Region (hg38): 17:74694311-74712978

Links

ENSG00000186074NCBI:146722OMIM:609807HGNC:29883Uniprot:Q8TDQ1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD300LF gene.

  • not_specified (31 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. These statistics are base on transcript: NM_000139018.5. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
26
clinvar
5
clinvar
31
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 26 6 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CD300LFprotein_codingprotein_codingENST00000326165 718666
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.06e-80.1821257080361257440.000143
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3581501630.9210.000008911860
Missense in Polyphen3234.4050.93009446
Synonymous-0.5847568.81.090.00000408584
Loss of Function0.3221314.30.9086.81e-7158

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009250.000925
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003560.0000352
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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