KLRG1

killer cell lectin like receptor G1, the group of Killer cell lectin like receptors|C-type lectin domain containing

Basic information

Region (hg38): 12:8950043-9010760

Links

ENSG00000139187 ∙ NCBI:10219 ∙ OMIM:604874 ∙ HGNC:6380 ∙ Uniprot:Q96E93 ∙ 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 KLRG1 gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRG1 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	6	1	1

Variants in KLRG1

This is a list of pathogenic ClinVar variants found in the KLRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-8989709-A-G		not specified	Uncertain significance (Jan 25, 2023)
12-8992287-T-C		not specified	Uncertain significance (Jan 26, 2022)
12-8995164-G-A		not specified	Likely benign (Feb 12, 2024)
12-8995272-C-T		not specified	Uncertain significance (Mar 23, 2022)
12-9009002-G-A		not specified	Uncertain significance (Dec 06, 2022)
12-9009003-C-A		not specified	Likely benign (Dec 06, 2022)
12-9009020-C-A		not specified	Uncertain significance (Dec 21, 2022)
12-9009523-A-G		not specified	Uncertain significance (Jun 11, 2021)
12-9010581-A-G			Benign (Feb 24, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRG1	protein_coding	protein_coding	ENST00000356986	5	60717

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00345	0.848	125698	0	9	125707	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.783	73	94.4	0.773	0.00000436	1228
Missense in Polyphen		13	23.847	0.54515		319
Synonymous	1.23	25	34.2	0.732	0.00000164	349
Loss of Function	1.21	5	8.88	0.563	3.76e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000440
Middle Eastern	0.00	0.00
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 and T-cell functions upon binding to their non-MHC ligands. May mediate missing self recognition by binding to a highly conserved site on classical cadherins, enabling it to monitor expression of E-cadherin/CDH1, N-cadherin/CDH2 and R-cadherin/CDH4 on target cells. {ECO:0000269|PubMed:19604491}.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Fc-epsilon receptor I signaling in mast cells (Consensus)

Recessive Scores

• pRec: 0.0518

Intolerance Scores

• loftool: 0.514
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.00881
• hipred: N
• hipred_score: 0.355
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.578

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klrg1
• Phenotype: normal phenotype

Gene ontology

• Biological process: inflammatory response;cellular defense response;cell surface receptor signaling pathway;innate immune response
• Cellular component: plasma membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;carbohydrate binding;signaling receptor activity