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.

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.

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			62	1	1	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	1	1

Variants in NKTR

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

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

Position	Type	Phenotype	Significance	ClinVar
3-42601014-C-T		not specified	Uncertain significance (Apr 07, 2023)
3-42619073-A-T		not specified	Uncertain significance (Apr 18, 2023)
3-42619091-A-G		not specified	Uncertain significance (May 26, 2024)
3-42621483-G-A		not specified	Uncertain significance (Apr 04, 2023)
3-42630559-G-T		not specified	Uncertain significance (Oct 30, 2024)
3-42631292-C-T		not specified	Uncertain significance (Mar 15, 2024)
3-42632664-C-T		not specified	Uncertain significance (Dec 21, 2022)
3-42632737-G-C		not specified	Uncertain significance (Oct 01, 2024)
3-42632751-G-A		not specified	Likely benign (Dec 14, 2023)
3-42633618-T-G			Benign (Dec 31, 2019)
3-42633720-C-T		not specified	Uncertain significance (Feb 05, 2024)
3-42634632-C-A		not specified	Uncertain significance (Oct 20, 2024)
3-42635247-A-T		not specified	Uncertain significance (Apr 27, 2024)
3-42635269-G-C		not specified	Uncertain significance (May 09, 2022)
3-42635320-A-G		not specified	Uncertain significance (Feb 05, 2024)
3-42635323-G-A		not specified	Uncertain significance (May 31, 2023)
3-42636891-G-A		not specified	Uncertain significance (May 26, 2024)
3-42636891-G-T		not specified	Uncertain significance (Jun 28, 2022)
3-42636939-A-G		not specified	Uncertain significance (Jun 07, 2023)
3-42636948-A-T		not specified	Uncertain significance (Jul 25, 2024)
3-42636992-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-42637002-A-C		not specified	Uncertain significance (Oct 29, 2021)
3-42637032-A-G		not specified	Uncertain significance (Jan 04, 2022)
3-42637080-T-G		not specified	Uncertain significance (Nov 15, 2021)
3-42637086-T-C		not specified	Uncertain significance (Dec 28, 2022)

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