KIR3DL2

killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2, the group of CD molecules|Killer cell immunoglobulin like receptors

Basic information

Region (hg38): 19:54850442-54867207

Links

ENSG00000240403 ∙ NCBI:3812 ∙ OMIM:604947 ∙ HGNC:6339 ∙ Uniprot:P43630 ∙ 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 KIR3DL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIR3DL2 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				3		3
missense			38	7		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	10	0

Variants in KIR3DL2

This is a list of pathogenic ClinVar variants found in the KIR3DL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54850498-T-C		not specified	Uncertain significance (Apr 17, 2023)
19-54850501-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-54852022-C-T		not specified	Uncertain significance (Oct 05, 2021)
19-54852027-C-G		not specified	Uncertain significance (Feb 15, 2023)
19-54852036-A-G		not specified	Likely benign (Jun 29, 2023)
19-54852060-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-54852066-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-54852082-G-A		not specified	Uncertain significance (Jul 20, 2022)
19-54852084-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-54852085-G-A		not specified	Uncertain significance (Apr 25, 2023)
19-54852103-T-C		not specified	Uncertain significance (May 26, 2024)
19-54852123-A-G		not specified	Uncertain significance (Sep 26, 2022)
19-54852124-G-T		not specified	Uncertain significance (Apr 23, 2024)
19-54852129-G-A		not specified	Uncertain significance (Feb 22, 2023)
19-54852165-T-C		not specified	Uncertain significance (May 10, 2022)
19-54852175-G-T		not specified	Uncertain significance (Jun 03, 2024)
19-54852216-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-54852223-G-A		not specified	Likely benign (Apr 25, 2023)
19-54852230-C-G		not specified	Uncertain significance (Sep 28, 2021)
19-54852235-T-C		not specified	Likely benign (Dec 20, 2021)
19-54853816-T-A		not specified	Uncertain significance (Jul 28, 2021)
19-54853822-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-54853828-C-T		not specified	Uncertain significance (May 15, 2023)
19-54853851-T-C		not specified	Likely benign (Dec 02, 2021)
19-54853893-G-A		not specified	Uncertain significance (Feb 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIR3DL2	protein_coding	protein_coding	ENST00000326321	9	16765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.08e-12	0.00902	125733	0	2	125735	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.74	243	178	1.37	0.0000101	2887
Missense in Polyphen		43	32.881	1.3078		598
Synonymous	-0.304	74	70.7	1.05	0.00000447	926
Loss of Function	-1.04	15	11.2	1.34	5.26e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor on natural killer (NK) cells for HLA-A alleles. 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);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Haploinsufficiency Scores

• pHI: 0.0636
• hipred: N
• hipred_score: 0.369
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kir3dl2

Gene ontology

• Biological process: cellular defense response;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: protein binding