CD300LF
CD300 molecule like family member f, the group of V-set domain containing
Basic information
Region (hg38): 17:74694311-74712978
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 14 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 4 | 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) | ||
| 17-74695793-G-T | not specified | Uncertain significance (Oct 07, 2024) | ||
| 17-74695838-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
| 17-74698467-T-C | not specified | Uncertain significance (Aug 28, 2024) | ||
| 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) | ||
| 17-74703065-G-T | not specified | Uncertain significance (Aug 27, 2024) | ||
| 17-74704537-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 17-74704569-A-C | not specified | Likely benign (May 01, 2024) | ||
| 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) | ||
| 17-74704756-G-A | not specified | Uncertain significance (Oct 21, 2024) | ||
| 17-74704787-G-A | not specified | Uncertain significance (Feb 28, 2024) |
GnomAD
Source:
| 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:
- 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