FOXM1

forkhead box M1, the group of Forkhead boxes

Basic information

Region (hg38): 12:2857680-2877174

Previous symbols: [ "FKHL16" ]

Links

ENSG00000111206 ∙ NCBI:2305 ∙ OMIM:602341 ∙ HGNC:3818 ∙ Uniprot:Q08050 ∙ 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 FOXM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXM1 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				2	4	6
missense			62	5	4	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	62	7	10

Variants in FOXM1

This is a list of pathogenic ClinVar variants found in the FOXM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-2858681-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-2858783-C-T		not specified	Uncertain significance (Feb 27, 2023)
12-2858786-T-C		not specified	Uncertain significance (Aug 21, 2023)
12-2858816-G-A		not specified	Uncertain significance (Jan 10, 2025)
12-2858849-G-A		not specified	Uncertain significance (Nov 10, 2024)
12-2858880-G-A		not specified	Uncertain significance (Sep 26, 2024)
12-2858894-G-A		not specified	Uncertain significance (Jun 10, 2024)
12-2858912-G-A			Likely benign (Feb 01, 2023)
12-2858924-G-C			Benign (Apr 19, 2018)
12-2858924-G-T		not specified	Uncertain significance (Jun 26, 2024)
12-2858928-G-T			Benign (Jan 08, 2018)
12-2858934-T-C		not specified	Uncertain significance (Aug 05, 2024)
12-2858955-G-A		not specified	Uncertain significance (Jan 28, 2025)
12-2858985-G-C		not specified	Uncertain significance (Nov 30, 2021)
12-2858999-T-C		not specified	Uncertain significance (Aug 20, 2024)
12-2859002-G-A		not specified	Uncertain significance (Jul 31, 2024)
12-2859015-G-A		not specified	Uncertain significance (Nov 09, 2021)
12-2859015-G-C		not specified	Uncertain significance (Dec 16, 2023)
12-2859049-C-T			Likely benign (Jun 20, 2018)
12-2859104-G-A		not specified	Uncertain significance (Sep 15, 2021)
12-2859111-G-T		not specified	Uncertain significance (Aug 28, 2023)
12-2859113-A-G		not specified	Uncertain significance (Nov 28, 2023)
12-2859116-G-A		not specified	Likely benign (Oct 05, 2021)
12-2859131-G-A		not specified	Uncertain significance (Sep 27, 2021)
12-2859180-G-T		not specified	Uncertain significance (Jan 20, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXM1	protein_coding	protein_coding	ENST00000342628	9	19360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000741	0.999	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.706	407	449	0.906	0.0000259	5187
Missense in Polyphen		107	132.91	0.80503		1610
Synonymous	-0.392	188	181	1.04	0.0000105	1658
Loss of Function	3.30	11	30.8	0.357	0.00000182	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000886	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional factor regulating the expression of cell cycle genes essential for DNA replication and mitosis. Plays a role in the control of cell proliferation. Plays also a role in DNA breaks repair participating in the DNA damage checkpoint response. {ECO:0000269|PubMed:17101782, ECO:0000269|PubMed:19160488, ECO:0000269|PubMed:20360045}.
• Pathway: Cellular senescence - Homo sapiens (human);EMT transition in Colorectal Cancer;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Polo-like kinase mediated events;Cyclin A/B1/B2 associated events during G2/M transition;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic;FOXM1 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.642

Intolerance Scores

• loftool: 0.0154
• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.7

Haploinsufficiency Scores

• pHI: 0.750
• hipred: Y
• hipred_score: 0.691
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.813

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxm1
• Phenotype: digestive/alimentary phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: foxm1
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;DNA repair;DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator;positive regulation of cell population proliferation;negative regulation of stress-activated MAPK cascade;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of Ras protein signal transduction;regulation of cell cycle;regulation of cell cycle arrest;negative regulation of cell aging;regulation of reactive oxygen species metabolic process;positive regulation of double-strand break repair
• Cellular component: nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;protein kinase binding