NKG7

natural killer cell granule protein 7

Basic information

Region (hg38): 19:51371605-51372701

Links

ENSG00000105374 ∙ NCBI:4818 ∙ OMIM:606008 ∙ HGNC:7830 ∙ Uniprot:Q16617 ∙ 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 NKG7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKG7 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			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	15	1	1

Variants in NKG7

This is a list of pathogenic ClinVar variants found in the NKG7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51371784-G-A		not specified	Uncertain significance (Jun 21, 2021)
19-51371800-G-C		not specified	Uncertain significance (Dec 06, 2021)
19-51371821-C-A		not specified	Uncertain significance (Jan 26, 2022)
19-51371824-G-T		not specified	Uncertain significance (May 30, 2023)
19-51371981-A-G		not specified	Uncertain significance (Oct 25, 2022)
19-51372008-T-C		not specified	Uncertain significance (Mar 07, 2024)
19-51372042-T-C			Benign (Dec 28, 2017)
19-51372063-C-A		not specified	Uncertain significance (Sep 19, 2022)
19-51372063-C-G		not specified	Uncertain significance (Nov 18, 2022)
19-51372176-C-T		not specified	Likely benign (Feb 23, 2023)
19-51372206-G-C		not specified	Uncertain significance (May 09, 2023)
19-51372248-C-T		not specified	Uncertain significance (Jul 14, 2022)
19-51372256-A-G		not specified	Uncertain significance (Mar 31, 2024)
19-51372277-A-T		not specified	Uncertain significance (Jun 22, 2021)
19-51372292-G-A		not specified	Uncertain significance (Jan 22, 2024)
19-51372311-A-T			Benign (Dec 28, 2017)
19-51372387-A-G		not specified	Uncertain significance (Oct 26, 2021)
19-51372473-A-C		not specified	Uncertain significance (Nov 01, 2022)
19-51372485-C-T		not specified	Likely benign (Mar 20, 2024)
19-51372502-C-T		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKG7	protein_coding	protein_coding	ENST00000221978	4	1110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000145	0.437	125731	0	14	125745	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0299	99	99.8	0.992	0.00000561	1039
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000712	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0935

Intolerance Scores

• loftool: 0.371
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.0638
• hipred: N
• hipred_score: 0.123
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00183

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkg7

Gene ontology

• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: protein binding