KIR2DL3

killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3, the group of CD molecules|Killer cell immunoglobulin like receptors

Basic information

Region (hg38): 19:54738513-54753052

Links

ENSG00000243772NCBI:3804OMIM:604938HGNC:6331Uniprot:P43628AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIR2DL3 gene.

  • not_specified (61 variants)
  • not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIR2DL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015868.3. 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
4
clinvar
4
missense
54
clinvar
7
clinvar
61
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 54 11 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KIR2DL3protein_codingprotein_codingENST00000342376 845797
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.68e-90.085112052212591205930.000294
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.682301691.360.000008852169
Missense in Polyphen8571.0781.1959996
Synonymous-3.5210467.31.550.00000401664
Loss of Function-0.08191312.71.025.37e-7175

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001790.00159
Ashkenazi Jewish0.002160.00161
East Asian0.0003330.000276
Finnish0.000.00
European (Non-Finnish)0.0001540.000119
Middle Eastern0.0003330.000276
South Asian0.00008140.0000692
Other0.0007350.000687

dbNSFP

Source: dbNSFP

Function
FUNCTION: Receptor on natural killer (NK) cells for HLA-C alleles (HLA-Cw1, HLA-Cw3 and HLA-Cw7). Inhibits the activity of NK cells thus preventing cell lysis.;
Pathway
Antigen processing and presentation - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

loftool
0.962
rvis_EVS
2.55
rvis_percentile_EVS
98.73

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.421
ghis
0.440

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.355

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
immune response;regulation of immune response
Cellular component
plasma membrane;integral component of plasma membrane;integral component of membrane
Molecular function
antigen binding;protein binding;signaling receptor activity