KIR3DL1

killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1, the group of CD molecules|Killer cell immunoglobulin like receptors

Basic information

Region (hg38): 19:54816468-54830778

Previous symbols: [ "KIR" ]

Links

ENSG00000167633 ∙ NCBI:3811 ∙ OMIM:604946 ∙ HGNC:6338 ∙ Uniprot:P43629 ∙ 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 KIR3DL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIR3DL1 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				1		1
missense			35	6		41
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	8	0

Variants in KIR3DL1

This is a list of pathogenic ClinVar variants found in the KIR3DL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54817565-C-A		not specified	Uncertain significance (Dec 16, 2021)
19-54818330-C-G		not specified	Uncertain significance (Sep 06, 2022)
19-54818344-T-C		not specified	Uncertain significance (Jan 12, 2024)
19-54818353-G-A		not specified	Uncertain significance (Jan 12, 2024)
19-54818366-G-A		not specified	Likely benign (Feb 02, 2022)
19-54818377-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-54818402-A-G		not specified	Uncertain significance (Oct 20, 2023)
19-54818489-T-C		not specified	Uncertain significance (Aug 11, 2022)
19-54818540-A-G		not specified	Uncertain significance (Dec 15, 2022)
19-54818552-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-54818581-G-A		Keratoconus	Uncertain significance (Apr 01, 2023)
19-54819767-G-A		not specified	Uncertain significance (May 14, 2024)
19-54819802-A-G		not specified	Likely benign (Dec 14, 2022)
19-54819832-G-T		Keratoconus	Uncertain significance (Apr 01, 2023)
19-54819842-AG-A			Likely benign (Dec 01, 2023)
19-54819844-G-A			Likely benign (Jul 01, 2022)
19-54819859-G-T		not specified	Uncertain significance (Oct 10, 2023)
19-54819893-A-G		not specified	Uncertain significance (Nov 15, 2021)
19-54819904-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-54819911-T-A		not specified	Uncertain significance (Aug 02, 2023)
19-54819929-G-A		not specified	Uncertain significance (Mar 12, 2024)
19-54819962-C-T		not specified	Uncertain significance (Sep 28, 2022)
19-54819970-C-G		not specified	Uncertain significance (Oct 18, 2021)
19-54819972-G-C		not specified	Uncertain significance (Jan 24, 2024)
19-54821573-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIR3DL1	protein_coding	protein_coding	ENST00000391728	9	142480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.36e-14	0.00517	118152	36	137	118325	0.000731

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.62	299	230	1.30	0.0000126	2840
Missense in Polyphen		40	38.708	1.0334		514
Synonymous	-1.46	107	89.5	1.20	0.00000521	874
Loss of Function	-0.857	18	14.5	1.24	6.77e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00205
Ashkenazi Jewish	0.00	0.00
East Asian	0.000968	0.000737
Finnish	0.0000997	0.0000992
European (Non-Finnish)	0.00116	0.000996
Middle Eastern	0.000968	0.000737
South Asian	0.000224	0.000149
Other	0.000356	0.000345

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor on natural killer (NK) cells for HLA Bw4 allele. Inhibits the activity of NK cells thus preventing cell lysis. {ECO:0000269|PubMed:22020283}.
• 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;Validated targets of C-MYC transcriptional activation (Consensus)

Intolerance Scores

• loftool: 0.972
• rvis_EVS: 3.34
• rvis_percentile_EVS: 99.43

Haploinsufficiency Scores

• pHI: 0.0581
• hipred: N
• hipred_score: 0.165
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0389

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: immune response;natural killer cell mediated cytotoxicity;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: amyloid-beta binding;protein binding;HLA-B specific inhibitory MHC class I receptor activity