KLRC3

protein-coding

killer cell lectin like receptor C3, the group of Killer cell lectin like receptors|C-type lectin domain containing

Gene summary

Natural killer (NK) cells are lymphocytes that can mediate lysis of certain tumor cells and virus-infected cells without previous activation. They can also regulate specific humoral and cell-mediated immunity. NK cells preferentially express several calcium-dependent (C-type) lectins, which have been implicated in the regulation of NK cell function. KLRC3 is a member of the NKG2 group which are expressed primarily in natural killer (NK) cells and encodes a family of transmembrane proteins characterized by a type II membrane orientation (extracellular C terminus) and the presence of a C-type lectin domain. The NKG2 gene family is located within the NK complex, a region that contains several C-type lectin genes preferentially expressed on NK cells. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002261.3

Inheritance

—

ClinVar variants

U:31B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr12:10,412,315-10,420,595

External References & Databases

Ensembl (ENSG00000205810)

Transcript & Mutation Effects

hg38 • Region Span ~8.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KLRC3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002261.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			29 clinvar	3 clinvar	1 clinvar	33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	31	3	1	35

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002261.3	RefSeq	NP_002252.2	7	MANE Select
ENST00000396439.7	Ensembl	ENSP00000379716.3	7	MANE Select
NM_007333.2	RefSeq	NP_031359.2	6	Standard
ENST00000381903.2	Ensembl	ENSP00000371328.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Antigen processing and presentation - Homo sapiens (human)
Natural killer cell mediated cytotoxicity - Homo sapiens (human)
ras-independent pathway in nk cell-mediated cytotoxicity
Validated nuclear estrogen receptor alpha network

Biological Process

cellular defense response

Molecular Function

transmembrane signaling receptor activity
carbohydrate binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381903
Coding exons: 6
Length: 8284
Individuals with no LoFs: 123694
Homozygous LoFs: 82
Heterozygous LoFs: 1839
Defined: 125615
p: 0.00768

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0202	118	117	1.01	0.00000592	1682
Missense (PolyPhen)		16	16.326	0.98004		253
Synonymous	-1.21	46	36.7	1.25	0.00000173	454
Loss of Function	0.116	9	9.38	0.959	3.97e-7	144

Population LoF Frequency

Population	CAF	p-value	Status
African	0.098	0.097	notable
Latino/Admixed American	0.0046	0.0046	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.0069	0.0069	notable
European (Non-Finnish)	0.00073	0.00072	rare
South Asian	0.00023	0.00023	rare
Other	0.0038	0.0038	notable

dbNSFP Gene Annotations

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.;

Intolerance Scores

LoFtool: 0.965
RVIS EVS: 0.64
RVIS percentile EVS: 83.78

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.526

Gene Damage Prediction

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