KIR2DL4

protein-coding

killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4, the group of CD molecules|Killer cell immunoglobulin like receptors

Gene summary

Killer cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several "framework" genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response. This gene is one of the "framework" loci that is present on all haplotypes. Alternate alleles of this gene are represented on multiple alternate reference loci (ALT_REF_LOCs). Alternative splicing results in multiple transcript variants, some of which may not be annotated on the primary reference assembly. [provided by RefSeq, Jul 2016]

MANE transcript

NM_001080770.2

Inheritance

—

ClinVar variants

U:50B:24

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr19:54,803,610-54,814,517

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~10.9 kb
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GenCC 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 KIR2DL4 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 57
not providedTotal: 19

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080770.2. 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.

EffectPLPVUSLBBSum
synonymous
19
clinvar
19
missense
50
clinvar
5
clinvar
55
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total005024074
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001080770.2RefSeqNP_001074239.17MANE Select
ENST00000345540.10EnsemblENSP00000339634.57MANE Select
NM_001080772.2RefSeqNP_001074241.17Standard
ENST00000346587.8EnsemblENSP00000345331.46Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Antigen processing and presentation - 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

Biological Process

  • positive regulation of natural killer cell cytokine production
  • cellular defense response
  • signal transduction
  • negative regulation of natural killer cell mediated cytotoxicity
  • regulation of immune response

Molecular Function

  • transmembrane signaling receptor activity
  • protein binding
  • MHC class Ib receptor activity

Cellular Component

  • plasma membrane
  • integral component of plasma membrane
  • membrane
  • early endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000345540
Coding exons
7
Length
89971
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2831021100.9240.000006072177
Missense (PolyPhen)1320.7730.6258535
Synonymous0.008174141.10.9980.00000245672
Loss of Function1.3336.740.4453.25e-7143

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Receptor on natural killer (NK) cells for HLA-C alleles. Inhibits the activity of NK cells thus preventing cell lysis.;

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.343

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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