KLRC4

killer cell lectin like receptor C4, the group of Killer cell lectin like receptors

Basic information

Region (hg38): 12:10403059-10409757

Links

ENSG00000183542 ∙ NCBI:8302 ∙ OMIM:602893 ∙ HGNC:6377 ∙ Uniprot:O43908 ∙ 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 KLRC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRC4 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			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in KLRC4

This is a list of pathogenic ClinVar variants found in the KLRC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10407672-G-C		not specified	Uncertain significance (Dec 15, 2023)
12-10407723-T-C		not specified	Uncertain significance (Mar 16, 2022)
12-10407786-C-T		not specified	Uncertain significance (May 24, 2023)
12-10408358-T-C			Benign (Aug 23, 2019)
12-10408370-A-T		not specified	Uncertain significance (Dec 27, 2023)
12-10408981-C-T		not specified	Uncertain significance (Jan 26, 2023)
12-10408993-C-G		not specified	Uncertain significance (Aug 08, 2022)
12-10409010-C-A		not specified	Uncertain significance (Mar 16, 2022)
12-10409457-T-C		not specified	Uncertain significance (Nov 07, 2022)
12-10409491-T-C		not specified	Uncertain significance (Jun 06, 2023)
12-10409511-C-G		not specified	Uncertain significance (Dec 01, 2022)
12-10409538-A-C		not specified	Uncertain significance (Oct 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRC4	protein_coding	protein_coding	ENST00000309384	4	2374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00568	0.738	125720	0	3	125723	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.508	66	78.7	0.839	0.00000362	1019
Missense in Polyphen		13	18.397	0.70663		287
Synonymous	-0.980	33	26.6	1.24	0.00000114	292
Loss of Function	0.810	4	6.17	0.648	2.59e-7	81

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	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as a receptor for the recognition of MHC class I HLA-E molecules by NK cells.
• Pathway: Antigen processing and presentation - Homo sapiens (human);ras-independent pathway in nk cell-mediated cytotoxicity (Consensus)

Recessive Scores

• pRec: 0.0676

Intolerance Scores

• loftool: 0.765
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.0568
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000222

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Cellular component: integral component of membrane