MKI67

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

Basic information

Region (hg38): 10:128096659-128126423

Links

ENSG00000148773 ∙ NCBI:4288 ∙ OMIM:176741 ∙ HGNC:7107 ∙ Uniprot:P46013 ∙ 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 MKI67 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MKI67 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				10	12	22
missense			188	31	13	232
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	189	41	25

Variants in MKI67

This is a list of pathogenic ClinVar variants found in the MKI67 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-128099234-T-G		MKI67-related disorder	Uncertain significance (Aug 15, 2023)
10-128101259-T-C			Benign (Dec 14, 2017)
10-128101280-C-T		not specified	Uncertain significance (Jul 08, 2022)
10-128101370-A-T		not specified	Uncertain significance (Mar 20, 2023)
10-128101371-T-A		not specified	Uncertain significance (Jun 11, 2024)
10-128101422-C-A		not specified	Uncertain significance (Sep 06, 2022)
10-128101542-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-128101572-T-A		not specified	Uncertain significance (Aug 16, 2021)
10-128101646-G-T		not specified	Uncertain significance (Jan 30, 2024)
10-128101680-G-A		not specified	Uncertain significance (May 04, 2022)
10-128102625-G-C		not specified	Uncertain significance (Apr 18, 2023)
10-128102688-C-A		not specified	Uncertain significance (Feb 28, 2023)
10-128102734-T-C		not specified	Uncertain significance (Jun 08, 2022)
10-128102736-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-128102737-G-T		not specified	Uncertain significance (Mar 31, 2023)
10-128102739-G-A		MKI67-related disorder	Uncertain significance (Feb 05, 2024)
10-128102744-C-A		not specified	Uncertain significance (Sep 17, 2021)
10-128102750-C-G		not specified	Uncertain significance (Mar 20, 2024)
10-128102800-A-G		not specified	Uncertain significance (Sep 23, 2023)
10-128102803-G-C		not specified	Uncertain significance (May 21, 2024)
10-128102899-C-T		not specified	Uncertain significance (Dec 19, 2023)
10-128102967-A-G		not specified	Likely benign (Nov 15, 2023)
10-128102979-T-A		not specified	Uncertain significance (Aug 30, 2022)
10-128102989-C-T		not specified	Uncertain significance (Feb 15, 2023)
10-128103034-T-C		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MKI67	protein_coding	protein_coding	ENST00000368654	14	29727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-28	0.999	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.68	1839	1.65e+3	1.12	0.0000902	21156
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.000236	0.000198
East Asian	0.00314	0.00283
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000719	0.0000703
Middle Eastern	0.00314	0.00283
South Asian	0.000140	0.000131
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: Primary Focal Segmental Glomerulosclerosis FSGS (Consensus)

Intolerance Scores

• loftool: 0.852
• rvis_EVS: 7.63
• rvis_percentile_EVS: 99.91

Haploinsufficiency Scores

• pHI: 0.624
• hipred: Y
• hipred_score: 0.598
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mki67
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell cycle;regulation of mitotic nuclear division;cell population proliferation;regulation of chromosome segregation;regulation of chromatin organization
• Cellular component: condensed chromosome;nucleus;nucleolus;membrane;nuclear body
• Molecular function: DNA binding;RNA binding;protein binding;ATP binding;protein C-terminus binding