NIM1K

NIM1 serine/threonine protein kinase

Basic information

Region (hg38): 5:43192071-43280850

Links

ENSG00000177453 ∙ NCBI:167359 ∙ ∙ HGNC:28646 ∙ Uniprot:Q8IY84 ∙ 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 NIM1K gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIM1K 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				1		1
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in NIM1K

This is a list of pathogenic ClinVar variants found in the NIM1K region.

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

Position	Type	Phenotype	Significance	ClinVar
5-43245795-A-G		not specified	Uncertain significance (Dec 09, 2023)
5-43245800-G-A		not specified	Uncertain significance (Feb 14, 2025)
5-43245828-G-A		not specified	Uncertain significance (Oct 29, 2024)
5-43245828-G-C		not specified	Uncertain significance (May 18, 2022)
5-43245842-G-A		not specified	Uncertain significance (Jan 04, 2025)
5-43245894-G-A		not specified	Uncertain significance (Jan 09, 2024)
5-43245902-C-T		not specified	Uncertain significance (Nov 25, 2024)
5-43245912-C-T		not specified	Uncertain significance (Aug 02, 2024)
5-43245914-C-T		not specified	Uncertain significance (Feb 11, 2022)
5-43245915-C-G		not specified	Uncertain significance (Feb 15, 2023)
5-43245972-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-43277102-A-C		not specified	Uncertain significance (Dec 27, 2023)
5-43277165-T-A		not specified	Uncertain significance (Feb 22, 2023)
5-43277168-G-A		not specified	Uncertain significance (Aug 05, 2024)
5-43277206-T-G		not specified	Uncertain significance (Jan 31, 2024)
5-43277219-A-G		not specified	Uncertain significance (Sep 11, 2024)
5-43277221-G-T		not specified	Uncertain significance (Oct 25, 2024)
5-43277243-G-T		not specified	Uncertain significance (Nov 14, 2024)
5-43277270-C-T		not specified	Uncertain significance (Dec 03, 2024)
5-43277275-C-T		not specified	Uncertain significance (Apr 23, 2024)
5-43279988-C-A		not specified	Uncertain significance (Apr 18, 2023)
5-43280028-T-C		not specified	Uncertain significance (Jan 17, 2024)
5-43280062-T-C		not specified	Uncertain significance (Dec 12, 2024)
5-43280096-G-A		not specified	Uncertain significance (Jul 14, 2023)
5-43280127-G-C		not specified	Uncertain significance (Feb 25, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIM1K	protein_coding	protein_coding	ENST00000512796	3	88780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.90e-12	0.0412	125645	0	103	125748	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0886	257	261	0.985	0.0000152	2867
Missense in Polyphen		83	89.386	0.92856		996
Synonymous	-0.756	112	102	1.10	0.00000627	852
Loss of Function	0.0897	18	18.4	0.977	0.00000127	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000904	0.000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000590	0.000589
Middle Eastern	0.000272	0.000272
South Asian	0.000196	0.000196
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.408
• ghis: 0.546

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nim1k

Gene ontology

• Biological process: protein phosphorylation;negative regulation of TOR signaling;intracellular signal transduction;cellular response to glucose starvation
• Cellular component: nucleus;cytoplasm;nucleotide-activated protein kinase complex
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;ATP binding