KIR2DL4

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

Basic information

Region (hg38): 19:54803610-54814517

Links

ENSG00000189013 ∙ NCBI:3805 ∙ OMIM:604945 ∙ HGNC:6332 ∙ Uniprot:Q99706 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIR2DL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIR2DL4 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				15		15
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	31	19	1

Variants in KIR2DL4

This is a list of pathogenic ClinVar variants found in the KIR2DL4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-54803665-C-T		not specified	Uncertain significance (Nov 09, 2022)
19-54803871-A-C		not specified	Benign (-)
19-54803893-T-A		not specified	Uncertain significance (Jul 05, 2023)
19-54803909-G-A		not specified	Uncertain significance (Jun 03, 2024)
19-54803914-T-C		not specified	Uncertain significance (Dec 18, 2023)
19-54803914-T-G		not specified	Uncertain significance (Mar 16, 2022)
19-54803917-G-A		not specified	Uncertain significance (Mar 07, 2023)
19-54803923-G-A		not specified	Uncertain significance (Jun 18, 2024)
19-54804801-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-54804837-G-C		not specified	Uncertain significance (Mar 12, 2024)
19-54804840-C-T		not specified	Uncertain significance (Apr 10, 2023)
19-54804847-G-A		not specified	Uncertain significance (Mar 19, 2024)
19-54804855-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-54804876-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-54804890-C-A		not specified	Uncertain significance (Aug 02, 2021)
19-54804892-T-C		not specified	Uncertain significance (Sep 14, 2022)
19-54804898-C-T		not specified	Uncertain significance (Sep 06, 2023)
19-54804909-A-G		not specified	Likely benign (Mar 17, 2023)
19-54804920-C-G			Likely benign (Aug 01, 2023)
19-54804959-T-C			Likely benign (Aug 01, 2023)
19-54804983-A-T			Likely benign (Aug 01, 2023)
19-54804989-C-G		not specified	Uncertain significance (Feb 06, 2024)
19-54805004-A-C		not specified	Uncertain significance (Jul 09, 2021)
19-54805010-A-G			Likely benign (Aug 01, 2023)
19-54805022-G-A			Likely benign (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIR2DL4	protein_coding	protein_coding	ENST00000345540	7	89971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0423	0.856	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.283	102	110	0.924	0.00000607	2177
Missense in Polyphen		13	20.773	0.6258		535
Synonymous	0.00817	41	41.1	0.998	0.00000245	672
Loss of Function	1.33	3	6.74	0.445	3.25e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0833
• hipred: N
• hipred_score: 0.380
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.343

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• 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;positive regulation of cellular senescence
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;early endosome membrane
• Molecular function: transmembrane signaling receptor activity;protein binding;MHC class Ib receptor activity