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): 19:54738512-54753052

Links

ENSG00000243772 ∙ NCBI:3804 ∙ OMIM:604938 ∙ HGNC:6331 ∙ Uniprot:P43628 ∙ 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 KIR2DL3 gene.

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.

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				2		2
missense			32	4		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	6	0

Variants in KIR2DL3

This is a list of pathogenic ClinVar variants found in the KIR2DL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54738551-G-A			Likely benign (May 01, 2022)
19-54738555-A-C		not specified	Uncertain significance (Jul 15, 2021)
19-54739521-C-A		not specified	Uncertain significance (May 16, 2023)
19-54739530-T-G		not specified	Uncertain significance (Sep 01, 2021)
19-54741976-C-T		Malignant tumor of prostate	Uncertain significance (-)
19-54741980-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-54742018-C-T		not specified	Uncertain significance (May 03, 2023)
19-54742022-T-A		not specified	Uncertain significance (Jan 16, 2024)
19-54742045-A-T		not specified	Uncertain significance (Dec 01, 2023)
19-54742070-G-T		not specified	Uncertain significance (Dec 03, 2021)
19-54742092-C-A		not specified	Uncertain significance (Mar 29, 2022)
19-54742110-G-C		not specified	Uncertain significance (Jun 17, 2022)
19-54742135-C-A		not specified	Uncertain significance (Apr 28, 2023)
19-54742172-G-T		not specified	Uncertain significance (Feb 07, 2023)
19-54742175-C-G		not specified	Uncertain significance (May 31, 2023)
19-54742181-T-C		not specified	Likely benign (May 31, 2023)
19-54742222-A-C		not specified	Uncertain significance (May 08, 2024)
19-54742227-C-G		not specified	Uncertain significance (Dec 08, 2023)
19-54742239-G-C		not specified	Uncertain significance (Dec 18, 2023)
19-54742250-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-54742269-C-G		not specified	Uncertain significance (Nov 18, 2022)
19-54743830-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-54743855-G-A		not specified	Likely benign (Jul 09, 2021)
19-54743887-T-C		not specified	Uncertain significance (Mar 06, 2023)
19-54743913-G-T		not specified	Uncertain significance (Jun 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIR2DL3	protein_coding	protein_coding	ENST00000342376	8	45797

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.68e-9	0.0851	120522	12	59	120593	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.68	230	169	1.36	0.00000885	2169
Missense in Polyphen		85	71.078	1.1959		996
Synonymous	-3.52	104	67.3	1.55	0.00000401	664
Loss of Function	-0.0819	13	12.7	1.02	5.37e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00179	0.00159
Ashkenazi Jewish	0.00216	0.00161
East Asian	0.000333	0.000276
Finnish	0.00	0.00
European (Non-Finnish)	0.000154	0.000119
Middle Eastern	0.000333	0.000276
South Asian	0.0000814	0.0000692
Other	0.000735	0.000687

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

• hipred: N
• hipred_score: 0.421
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

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

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