KLRD1

killer cell lectin like receptor D1, the group of Killer cell lectin like receptors|C-type lectin domain containing|CD molecules

Basic information

Region (hg38): 12:10226057-10329608

Previous symbols: [ "CD94" ]

Links

ENSG00000134539 ∙ NCBI:3824 ∙ OMIM:602894 ∙ HGNC:6378 ∙ Uniprot:Q13241 ∙ 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 KLRD1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRD1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in KLRD1

This is a list of pathogenic ClinVar variants found in the KLRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10311479-C-A		not specified	Uncertain significance (Jan 09, 2024)
12-10311559-C-A		not specified	Uncertain significance (Dec 16, 2022)
12-10311587-T-G		not specified	Uncertain significance (Sep 16, 2021)
12-10311605-C-T		not specified	Uncertain significance (Apr 13, 2022)
12-10311607-G-C		not specified	Uncertain significance (Feb 27, 2023)
12-10313423-C-G		not specified	Uncertain significance (Feb 28, 2024)
12-10314713-G-T		not specified	Uncertain significance (Aug 11, 2022)
12-10314768-A-C		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRD1	protein_coding	protein_coding	ENST00000336164	6	91194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000875	0.808	125701	0	7	125708	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.430	81	92.6	0.874	0.00000462	1185
Missense in Polyphen		22	24.964	0.88128		337
Synonymous	0.971	27	34.2	0.789	0.00000196	302
Loss of Function	1.11	6	9.75	0.615	4.13e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as a receptor for the recognition of MHC class I HLA-E molecules by NK cells and some cytotoxic T-cells.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);DAP12 signaling;DAP12 interactions;ras-independent pathway in nk cell-mediated cytotoxicity;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.242

Intolerance Scores

• loftool: 0.849
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.0993
• hipred: N
• hipred_score: 0.112
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.637

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klrd1

Gene ontology

• Biological process: natural killer cell mediated immunity;cell surface receptor signaling pathway;innate immune response;regulation of immune response
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane;receptor complex
• Molecular function: transmembrane signaling receptor activity;protein binding;MHC class I protein complex binding;MHC class Ib protein binding, via antigen binding groove;carbohydrate binding;protein antigen binding