NIM1K

protein-coding

NIM1 serine/threonine protein kinase

Gene summary

Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Predicted to be involved in intracellular signal transduction. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_153361.4

Inheritance

—

ClinVar variants

U:57B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr5:43,192,071-43,280,850

External References & Databases

Ensembl (ENSG00000177453)

Transcript & Mutation Effects

hg38 • Region Span ~88.8 kb

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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 NIM1K variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153361.4. 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				2 clinvar		2
missense			57 clinvar			57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	2	0	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153361.4	RefSeq	NP_699192.1	3	MANE Select
ENST00000326035.6	Ensembl	ENSP00000313572.2	3	MANE Select
ENST00000512796.1	Ensembl	ENSP00000420849.1	3	Standard
ENST00000512796.2	Ensembl	ENSP00000420849.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
negative regulation of TOR signaling
intracellular signal transduction
cellular response to glucose starvation

Molecular Function

magnesium ion binding
protein serine/threonine kinase activity
ATP binding

Cellular Component

nucleus
cytoplasm
nucleotide-activated protein kinase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000512796
Coding exons: 3
Length: 88780
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 103
Defined: 125748
p: 0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0886	257	261	0.985	0.0000152	2867
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00059	0.00059	rare
South Asian	0.00020	0.00020	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.56
RVIS percentile EVS: 19.73

Essentials

Essential (gene trap): N

Gene Damage Prediction

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