NCR2

protein-coding

natural cytotoxicity triggering receptor 2, the group of V-set domain containing|CD molecules

Gene summary

Predicted to enable signaling receptor activity. Predicted to be involved in cellular defense response and signal transduction. Predicted to be located in plasma membrane. Predicted to be active in cell surface. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

LY95

MANE transcript

NM_004828.4

Inheritance

—

ClinVar variants

U:40B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr6:41,335,608-41,350,889

External References & Databases

Ensembl (ENSG00000096264)

Transcript & Mutation Effects

hg38 • Region Span ~15.3 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 NCR2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004828.4. 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					1 clinvar	1
missense			40 clinvar	4 clinvar	2 clinvar	46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	4	3	47

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004828.4	RefSeq	NP_004819.2	5	MANE Select
ENST00000373089.10	Ensembl	ENSP00000362181.5	5	MANE Select
NM_001199509.2	RefSeq	NP_001186438.1	6	Standard
NM_001199510.2	RefSeq	NP_001186439.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Natural killer cell mediated cytotoxicity - Homo sapiens (human)
DAP12 interactions
Innate Immune System
Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

Biological Process

cellular defense response
signal transduction
innate immune response
regulation of immune response

Molecular Function

transmembrane signaling receptor activity
protein binding

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373089
Coding exons: 5
Length: 15233
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.191	149	156	0.957	0.00000843	1736
Missense (PolyPhen)		22	24.733	0.8895		288
Synonymous	-1.26	79	66.0	1.20	0.00000400	589
Loss of Function	0.425	11	12.6	0.871	6.92e-7	116

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00058	0.00058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00052	0.00052	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cytotoxicity-activating receptor that may contribute to the increased efficiency of activated natural killer (NK) cells to mediate tumor cell lysis. {ECO:0000269|PubMed:10049942}.;

Recessive Scores

pRec: 0.161

Intolerance Scores

LoFtool: 0.742
RVIS EVS: 1.24
RVIS percentile EVS: 93.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0000648

Gene Damage Prediction

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