KLRK1
killer cell lectin like receptor K1, the group of CD molecules|Killer cell lectin like receptors|C-type lectin domain containing
Basic information
Region (hg38): 12:10372353-10391874
Previous symbols: [ "D12S2489E" ]
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 KLRK1 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 | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 1 | 0 | 1 |
Variants in KLRK1
This is a list of pathogenic ClinVar variants found in the KLRK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-10372766-G-C | Benign (Jan 18, 2019) | |||
| 12-10388791-C-T | not specified | Uncertain significance (Feb 10, 2023) | ||
| 12-10388798-G-A | not specified | Uncertain significance (May 29, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KLRK1 | protein_coding | protein_coding | ENST00000240618 | 7 | 19522 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.98e-14 | 0.00465 | 125690 | 0 | 54 | 125744 | 0.000215 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.631 | 94 | 113 | 0.833 | 0.00000566 | 1435 |
| Missense in Polyphen | 19 | 24.359 | 0.78001 | 304 | ||
| Synonymous | -0.146 | 35 | 33.9 | 1.03 | 0.00000159 | 346 |
| Loss of Function | -0.911 | 18 | 14.3 | 1.26 | 6.74e-7 | 166 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000214 | 0.000214 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000275 | 0.000272 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.000337 | 0.000334 |
| Middle Eastern | 0.000275 | 0.000272 |
| South Asian | 0.000150 | 0.000131 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Function as an activating and costimulatory receptor involved in immunosurveillance upon binding to various cellular stress-inducible ligands displayed at the surface of autologous tumor cells and virus-infected cells. Provides both stimulatory and costimulatory innate immune responses on activated killer (NK) cells, leading to cytotoxic activity. Acts as a costimulatory receptor for T-cell receptor (TCR) in CD8(+) T-cell-mediated adaptive immune responses by amplifying T-cell activation. Stimulates perforin-mediated elimination of ligand-expressing tumor cells. Signaling involves calcium influx, culminating in the expression of TNF-alpha. Participates in NK cell-mediated bone marrow graft rejection. May play a regulatory role in differentiation and survival of NK cells. Binds to ligands belonging to various subfamilies of MHC class I-related glycoproteins including MICA, MICB, RAET1E, RAET1G, RAET1L/ULBP6, ULBP1, ULBP2, ULBP3 (ULBP2>ULBP1>ULBP3) and ULBP4. {ECO:0000269|PubMed:10426994, ECO:0000269|PubMed:11224526, ECO:0000269|PubMed:11777960, ECO:0000269|PubMed:15240696, ECO:0000269|PubMed:19658097, ECO:0000269|PubMed:21898152, ECO:0000269|PubMed:23298206, ECO:0000269|PubMed:28559451}.;
- Pathway
- Malaria - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);DAP12 signaling;DAP12 interactions;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.282
Intolerance Scores
- loftool
- 0.801
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.106
- hipred
- N
- hipred_score
- 0.133
- ghis
- 0.379
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.433
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Klrk1
- Phenotype
- immune system phenotype; neoplasm; 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
- stimulatory C-type lectin receptor signaling pathway;adaptive immune response;positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target;signal transduction;natural killer cell activation;cell differentiation;positive regulation of myeloid dendritic cell activation;T cell costimulation;positive regulation of interferon-gamma production;negative regulation of GTPase activity;natural killer cell mediated cytotoxicity;positive regulation of apoptotic process;positive regulation of nitric oxide biosynthetic process;positive regulation of natural killer cell mediated cytotoxicity;regulation of immune response;defense response to Gram-positive bacterium;cellular response to lipopolysaccharide;negative regulation of natural killer cell chemotaxis
- Cellular component
- plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;integral component of membrane
- Molecular function
- protein binding;kinase binding;carbohydrate binding;MHC class Ib receptor activity;signaling receptor activity;MHC class I protein binding;protein homodimerization activity