KIR3DL3

killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3, the group of CD molecules|Killer cell immunoglobulin like receptors

Basic information

Region (hg38): 19:54724442-54736632

Links

ENSG00000242019 ∙ NCBI:115653 ∙ OMIM:610095 ∙ HGNC:16312 ∙ Uniprot:Q8N743 ∙ 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 KIR3DL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIR3DL3 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			36	4	1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	5	1

Variants in KIR3DL3

This is a list of pathogenic ClinVar variants found in the KIR3DL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54724501-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-54724519-T-C		not specified	Uncertain significance (Nov 09, 2021)
19-54726151-G-A		not specified	Uncertain significance (Mar 29, 2022)
19-54726196-T-C		not specified	Uncertain significance (Dec 28, 2022)
19-54726201-C-G		not specified	Uncertain significance (Jan 26, 2022)
19-54726212-G-A		not specified	Uncertain significance (May 25, 2022)
19-54726280-C-G		not specified	Uncertain significance (Apr 25, 2022)
19-54726302-C-T		not specified	Uncertain significance (Nov 21, 2023)
19-54726308-C-T		not specified	Uncertain significance (Nov 12, 2021)
19-54726319-G-C		not specified	Likely benign (Jun 29, 2023)
19-54727662-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-54727667-G-C		not specified	Uncertain significance (Jan 04, 2022)
19-54727682-C-A		not specified	Uncertain significance (Aug 13, 2021)
19-54727686-G-A		not specified	Uncertain significance (Feb 12, 2024)
19-54727746-C-A		not specified	Uncertain significance (Dec 07, 2021)
19-54727752-G-A		not specified	Likely benign (Jul 22, 2022)
19-54727771-C-T			Likely benign (Mar 01, 2023)
19-54727776-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-54727901-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-54729526-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-54729576-C-T		not specified	Uncertain significance (Feb 13, 2023)
19-54729612-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-54729649-G-T		not specified	Uncertain significance (Nov 22, 2022)
19-54729679-C-T		not specified	Uncertain significance (Mar 16, 2022)
19-54729715-G-A		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIR3DL3	protein_coding	protein_coding	ENST00000291860	8	12020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000121	0.402	110944	0	6	110950	0.0000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.261	118	110	1.07	0.00000598	2623
Missense in Polyphen		24	20.906	1.148		671
Synonymous	0.963	34	41.9	0.811	0.00000239	836
Loss of Function	0.121	6	6.33	0.948	2.67e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000774	0.0000742
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000555
Finnish	0.0000525	0.0000506
European (Non-Finnish)	0.00000997	0.00000990
Middle Eastern	0.0000556	0.0000555
South Asian	0.0000835	0.0000829
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor on natural killer cells. May inhibit the activity of NK cells thus preventing cell lysis. {ECO:0000303|PubMed:11513144}.
• Pathway: Antigen processing and presentation - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

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

• Cellular component: plasma membrane;integral component of membrane