NKG7

protein-coding

natural killer cell granule protein 7

Gene summary

Involved in defense response to protozoan. Located in cytolytic granule membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_005601.4

Inheritance

—

ClinVar variants

U:32B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr19:51,371,606-51,372,701

External References & Databases

Ensembl (ENSG00000105374)

Transcript & Mutation Effects

hg38 • Region Span ~1.1 kb

Loading mutation effect viewer...

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 NKG7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005601.4. 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			30 clinvar	4 clinvar	1 clinvar	35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	32	4	1	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005601.4	RefSeq	NP_005592.1	4	MANE Select
ENST00000221978.10	Ensembl	ENSP00000221978.4	4	MANE Select
NM_001363693.2	RefSeq	NP_001350622.1	3	Standard
ENST00000593572.5	Ensembl	ENSP00000473204.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000221978
Coding exons: 4
Length: 1110
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125745
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0299	99	99.8	0.992	0.00000561	1039
Missense (PolyPhen)		45	49.746	0.90459		522
Synonymous	-0.122	45	44.0	1.02	0.00000267	359
Loss of Function	0.215	6	6.60	0.910	2.82e-7	67

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0935

Intolerance Scores

LoFtool: 0.371
RVIS EVS: 0.13
RVIS percentile EVS: 63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00183

Gene Damage Prediction

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