NKTR

natural killer cell triggering receptor, the group of Cyclophilin peptidylprolyl isomerases

Basic information

Region (hg38): 3:42600655-42648735

Links

ENSG00000114857 ∙ NCBI:4820 ∙ OMIM:161565 ∙ HGNC:7833 ∙ Uniprot:P30414 ∙ 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 NKTR gene.

• not_specified (155 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKTR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005385.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			152	3	1	156
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	152	4	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKTR	protein_coding	protein_coding	ENST00000232978	16	48122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.940	0.0597	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	661	764	0.865	0.0000398	9579
Missense in Polyphen		125	151.1	0.82724		2053
Synonymous	0.436	258	267	0.966	0.0000133	2717
Loss of Function	6.42	15	75.1	0.200	0.00000497	910

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000524	0.000515
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.0000625	0.0000544
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000188	0.000185
Middle Eastern	0.0000625	0.0000544
South Asian	0.000277	0.000261
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:20676357). Component of a putative tumor-recognition complex involved in the function of NK cells (PubMed:8421688). {ECO:0000269|PubMed:20676357, ECO:0000269|PubMed:8421688}.

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.493
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.76

Haploinsufficiency Scores

• pHI: 0.481
• hipred: N
• hipred_score: 0.492
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nktr

Gene ontology

• Biological process: protein peptidyl-prolyl isomerization;protein refolding
• Cellular component: nucleoplasm;mitochondrion;cytosol;plasma membrane
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;cyclosporin A binding;unfolded protein binding