MKI67

protein-coding

marker of proliferation Ki-67, the group of Protein phosphatase 1 regulatory subunits

Gene summary

Enables RNA binding activity and molecular condensate scaffold activity. Involved in chromosome segregation and regulation of mitotic nuclear division. Located in chromosome; nucleolus; and nucleoplasm. Is active in condensed chromosome. Implicated in several diseases, including Crohn's disease; colorectal cancer; endocrine gland cancer (multiple); graft-versus-host disease; and human immunodeficiency virus infectious disease. Biomarker of several diseases, including Barrett's esophagus; endocrine gland cancer (multiple); gastrointestinal system cancer (multiple); interstitial cystitis; and lung cancer (multiple). [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_002417.5

Inheritance

—

ClinVar variants

U:494B:96

Top phenotype

MKI67-related disorder

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr10:128,096,659-128,126,423

External References & Databases

Ensembl (ENSG00000148773)

Transcript & Mutation Effects

hg38 • Region Span ~29.8 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 MKI67 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 527

not providedTotal: 46

MKI67-related disorderTotal: 16

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002417.5. 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			3 clinvar	12 clinvar	11 clinvar	26
missense			484 clinvar	62 clinvar	11 clinvar	557
nonsense			6 clinvar			6
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	494	74	22	590

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002417.5	RefSeq	NP_002408.3	14	MANE Select
ENST00000368654.8	Ensembl	ENSP00000357643.3	14	MANE Select
NM_001145966.2	RefSeq	NP_001139438.1	13	Standard
ENST00000368653.7	Ensembl	ENSP00000357642.3	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Primary Focal Segmental Glomerulosclerosis FSGS

Biological Process

cell cycle
regulation of mitotic nuclear division
cell population proliferation
regulation of chromosome segregation
regulation of chromatin organization

Molecular Function

DNA binding
RNA binding
protein binding
ATP binding
protein C-terminus binding

Cellular Component

condensed chromosome
nucleus
nucleolus
membrane
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368654
Coding exons: 14
Length: 29727
Individuals with no LoFs: 125672
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 125748
p: 0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.68	1839	1.65e+3	1.12	0.0000902	21156
Missense (PolyPhen)		455	446.97	1.018		6303
Synonymous	-2.90	709	617	1.15	0.0000355	6575
Loss of Function	3.52	61	98.8	0.618	0.00000532	1447

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00024	0.00020	rare
East Asian	0.0031	0.0028	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0.00014	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly (PubMed:27362226). Associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface (PubMed:27362226). Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility (PubMed:27362226). Binds DNA, with a preference for supercoiled DNA and AT-rich DNA (PubMed:10878551). Does not contribute to the internal structure of mitotic chromosomes (By similarity). May play a role in chromatin organization (PubMed:24867636). It is however unclear whether it plays a direct role in chromatin organization or whether it is an indirect consequence of its function in maintaining mitotic chromosomes dispersed (Probable). {ECO:0000250|UniProtKB:E9PVX6, ECO:0000269|PubMed:10878551, ECO:0000269|PubMed:24867636, ECO:0000269|PubMed:27362226}.;

Intolerance Scores

LoFtool: 0.852
RVIS EVS: 7.63
RVIS percentile EVS: 99.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.394

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High