KLRB1

killer cell lectin like receptor B1, the group of Killer cell lectin like receptors|C-type lectin domain containing|CD molecules

Basic information

Region (hg38): 12:9594551-9607916

Previous symbols: [ "NKR" ]

Links

ENSG00000111796 ∙ NCBI:3820 ∙ OMIM:602890 ∙ HGNC:6373 ∙ Uniprot:Q12918 ∙ 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 KLRB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRB1 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						0
missense			16	1		17
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	16	1	0

Variants in KLRB1

This is a list of pathogenic ClinVar variants found in the KLRB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-9595311-A-C		not specified	Uncertain significance (Jan 04, 2022)
12-9598115-A-G		not specified	Uncertain significance (Jan 31, 2023)
12-9598147-G-C		not specified	Uncertain significance (Jun 13, 2024)
12-9598507-C-T		not specified	Uncertain significance (May 08, 2024)
12-9598530-C-G		not specified	Uncertain significance (Sep 22, 2023)
12-9598613-T-G		not specified	Uncertain significance (Mar 14, 2023)
12-9598638-A-G		not specified	Uncertain significance (Mar 23, 2023)
12-9598647-G-A		not specified	Uncertain significance (Mar 18, 2024)
12-9599773-T-G		not specified	Uncertain significance (Jun 24, 2022)
12-9599777-A-C		not specified	Uncertain significance (Jun 22, 2024)
12-9599780-C-G		not specified	Uncertain significance (Jan 19, 2024)
12-9599817-G-A		not specified	Uncertain significance (Jul 05, 2023)
12-9599826-T-C		not specified	Uncertain significance (Oct 29, 2021)
12-9601511-C-A		not specified	Uncertain significance (Jul 19, 2023)
12-9601513-A-T		not specified	Uncertain significance (Dec 28, 2023)
12-9601536-A-G		not specified	Uncertain significance (Feb 28, 2024)
12-9601549-C-T		not specified	Uncertain significance (Mar 18, 2024)
12-9601567-C-A		not specified	Uncertain significance (Feb 15, 2023)
12-9601593-C-A		not specified	Uncertain significance (Jan 10, 2022)
12-9607747-C-T			Likely benign (May 29, 2018)
12-9607766-G-T		not specified	Uncertain significance (Oct 12, 2022)
12-9607767-A-G		not specified	Uncertain significance (Feb 28, 2023)
12-9607767-A-T			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRB1	protein_coding	protein_coding	ENST00000229402	6	13336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.41e-7	0.293	125716	0	8	125724	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.133	106	110	0.964	0.00000521	1449
Missense in Polyphen		15	25.836	0.58059		392
Synonymous	0.865	33	40.0	0.826	0.00000189	415
Loss of Function	0.417	11	12.6	0.873	6.85e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000930	0.0000929
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an inhibitory role on natural killer (NK) cells cytotoxicity. Activation results in specific acid sphingomyelinase/SMPD1 stimulation with subsequent marked elevation of intracellular ceramide. Activation also leads to AKT1/PKB and RPS6KA1/RSK1 kinases stimulation as well as markedly enhanced T-cell proliferation induced by anti-CD3. Acts as a lectin that binds to the terminal carbohydrate Gal-alpha(1,3)Gal epitope as well as to the N-acetyllactosamine epitope. Binds also to CLEC2D/LLT1 as a ligand and inhibits NK cell-mediated cytotoxicity as well as interferon-gamma secretion in target cells. {ECO:0000269|PubMed:16455998, ECO:0000269|PubMed:16925668, ECO:0000269|PubMed:8077657}.
• Pathway: Malaria - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.803
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.0854
• hipred: N
• hipred_score: 0.112
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0670

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klrb1c

Gene ontology

• Biological process: cell surface receptor signaling pathway;regulation of immune response
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: transmembrane signaling receptor activity;protein binding;carbohydrate binding