KIR2DL1

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

Basic information

Region (hg38): 19:54769793-54784322

Links

ENSG00000125498 ∙ NCBI:3802 ∙ OMIM:604936 ∙ HGNC:6329 ∙ Uniprot:P43626 ∙ 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 KIR2DL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIR2DL1 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				4		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	0	6	0

Variants in KIR2DL1

This is a list of pathogenic ClinVar variants found in the KIR2DL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54773369-G-A			Likely benign (Oct 01, 2024)
19-54773372-G-C		KIR2DL1-related disorder	Benign (Jun 15, 2021)
19-54773406-G-A		KIR2DL1-related disorder	Likely benign (Apr 14, 2021)
19-54773524-A-G		KIR2DL1-related disorder	Likely benign (Feb 18, 2022)
19-54773534-C-A		Keratoconus	Uncertain significance (Apr 01, 2023)
19-54773535-G-A		KIR2DL1-related disorder	Likely benign (Aug 01, 2023)
19-54773601-T-G			Likely benign (Aug 01, 2023)
19-54773629-A-G			Likely benign (Jul 01, 2022)
19-54775213-T-A		KIR2DL1-related disorder	Likely benign (Feb 28, 2022)
19-54775315-G-T		KIR2DL1-related disorder	Likely benign (Feb 28, 2022)
19-54775318-C-G		KIR2DL1-related disorder	Likely benign (Feb 28, 2022)
19-54780090-G-A			Likely benign (Dec 01, 2024)
19-54780161-G-C			Likely benign (Mar 01, 2025)
19-54783716-G-A		KIR2DL1-related disorder	Likely benign (Feb 10, 2022)
19-54783763-A-G		KIR2DL1-related disorder	Likely benign (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIR2DL1	protein_coding	protein_coding	ENST00000336077	8	14512

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.57e-15	0.00155	122628	2	19	122649	0.0000856

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.10	262	182	1.44	0.0000101	2199
Missense in Polyphen		98	73.611	1.3313		1024
Synonymous	-3.20	108	73.1	1.48	0.00000449	684
Loss of Function	-1.34	19	13.7	1.39	6.42e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000259	0.000248
Ashkenazi Jewish	0.000106	0.000105
East Asian	0.000112	0.000110
Finnish	0.00	0.00
European (Non-Finnish)	0.0000748	0.0000720
Middle Eastern	0.000112	0.000110
South Asian	0.000262	0.000169
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor on natural killer (NK) cells for some HLA-C alleles such as w4 and w6. Inhibits the activity of NK cells thus preventing cell lysis. {ECO:0000269|PubMed:18604210}.
• 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: 0.974
• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.509

Gene Damage Prediction

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

Gene ontology

• Biological process: natural killer cell inhibitory signaling pathway;immune response;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: protein binding;signaling receptor activity