NCR3LG1

protein-coding

natural killer cell cytotoxicity receptor 3 ligand 1, the group of Receptor ligands|B7 family|C1-set domain containing

Gene summary

B7H6 belongs to the B7 family (see MIM 605402) and is selectively expressed on tumor cells. Interaction of B7H6 with NKp30 (NCR3; MIM 611550) results in natural killer (NK) cell activation and cytotoxicity (Brandt et al., 2009 [PubMed 19528259]).[supplied by OMIM, Jan 2011]

MANE transcript

NM_001202439.3

Inheritance

—

ClinVar variants

U:40B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr11:17,351,800-17,377,341

External References & Databases

Ensembl (ENSG00000188211)

Transcript & Mutation Effects

hg38 • Region Span ~25.5 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 NCR3LG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001202439.3. 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				2 clinvar		2
missense			40 clinvar	4 clinvar		44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	6	0	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001202439.3	RefSeq	NP_001189368.1	5	MANE Select
ENST00000338965.9	Ensembl	ENSP00000341637.4	5	MANE Select
ENST00000530403.1	Ensembl	ENSP00000434394.1	5	Standard
ENST00001112435.1	Ensembl	ENSP00000782240.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

regulation of immune response

Molecular Function

structural molecule activity
protein binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000338965
Coding exons: 5
Length: 25616
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.69	157	229	0.686	0.0000111	2926
Missense (PolyPhen)		24	47.956	0.50046		643
Synonymous	1.58	74	93.4	0.792	0.00000482	922
Loss of Function	1.18	8	12.5	0.641	6.98e-7	143

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Triggers NCR3-dependent natural killer cell activation. {ECO:0000269|PubMed:19528259}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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