KLRD1
protein-codingkiller cell lectin like receptor D1, the group of Killer cell lectin like receptors|C-type lectin domain containing|CD molecules
Gene summary
Natural killer (NK) cells are a distinct lineage of lymphocytes that mediate cytotoxic activity and secrete cytokines upon immune stimulation. Several genes of the C-type lectin superfamily, including members of the NKG2 family, are expressed by NK cells and may be involved in the regulation of NK cell function. KLRD1 (CD94) is an antigen preferentially expressed on NK cells and is classified as a type II membrane protein because it has an external C terminus. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2017]
- CD94
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~103.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KLRD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002262.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 15 | 3 | 18 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 16 | 3 | 0 | 19 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002253.2 | 6 | MANE Select | |
| Ensembl | ENSP00000338130.4 | 6 | MANE Select | |
| RefSeq | NP_001107868.2 | 6 | Standard | |
| RefSeq | NP_001337989.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Antigen processing and presentation - Homo sapiens (human)
- Graft-versus-host disease - Homo sapiens (human)
- Natural killer cell mediated cytotoxicity - Homo sapiens (human)
- DAP12 signaling
- DAP12 interactions
Biological Process
- natural killer cell mediated immunity
- cell surface receptor signaling pathway
- innate immune response
- regulation of immune response
Molecular Function
- transmembrane signaling receptor activity
- protein binding
- MHC class I protein complex binding
- MHC class Ib protein binding, via antigen binding groove
- carbohydrate binding
Cellular Component
- plasma membrane
- external side of plasma membrane
- integral component of membrane
- receptor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000336164
- Coding exons
- 6
- Length
- 91194
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125708
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.430 | 81 | 92.6 | 0.874 | 0.00000462 | 1185 |
| Missense (PolyPhen) | 22 | 24.964 | 0.88128 | 337 | ||
| Synonymous | 0.971 | 27 | 34.2 | 0.789 | 0.00000196 | 302 |
| Loss of Function | 1.11 | 6 | 9.75 | 0.615 | 4.13e-7 | 113 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role as a receptor for the recognition of MHC class I HLA-E molecules by NK cells and some cytotoxic T-cells.;
Recessive Scores
- pRec
- 0.242
Intolerance Scores
- LoFtool
- 0.849
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 74.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.637
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |