KIR3DL1

protein-coding

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

Gene summary

Killer cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several "framework" genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response. [provided by RefSeq, Jul 2008]

Previous symbols:

MANE transcript

NM_013289.4

Inheritance

—

ClinVar variants

U:81B:9

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 1.24

Max pathogenic AF

—

Genomic locus

chr19:54,816,468-54,830,778

External References & Databases

Ensembl (ENSG00000167633)

Transcript & Mutation Effects

hg38 • Region Span ~14.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIR3DL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 5

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013289.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			80 clinvar	7 clinvar		87
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	81	9	0	90

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013289.4	RefSeq	NP_037421.2	9	MANE Select
ENST00000391728.8	Ensembl	ENSP00000375608.4	9	MANE Select
ENST00000326542.11	Ensembl	ENSP00000326868.7	8	Standard
ENST00000326542.12	Ensembl	ENSP00000326868.7	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

immune response
natural killer cell mediated cytotoxicity
regulation of immune response

Molecular Function

amyloid-beta binding
protein binding
HLA-B specific inhibitory MHC class I receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000391728
Coding exons: 9
Length: 142480
Individuals with no LoFs: 118152
Homozygous LoFs: 36
Heterozygous LoFs: 137
Defined: 118325
p: 0.000731

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.62	299	230	1.30	0.0000126	2840
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00090	0.00068	rare
Latino/Admixed American	0.0014	0.0010	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00097	0.00074	rare
Finnish	0.00010	0.000099	rare
European (Non-Finnish)	0.0012	0.0010	notable
South Asian	0.00022	0.00015	rare
Other	0.00036	0.00034	rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.972
RVIS EVS: 3.34
RVIS percentile EVS: 99.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0389

Gene Damage Prediction

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