FOXF2

forkhead box F2, the group of Forkhead boxes

Basic information

Region (hg38): 6:1389576-1395603

Previous symbols: [ "FKHL6" ]

Links

ENSG00000137273 ∙ NCBI:2295 ∙ OMIM:603250 ∙ HGNC:3810 ∙ Uniprot:Q12947 ∙ 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 FOXF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXF2 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				5	2	7
missense			25	3		28
nonsense						0
start loss						0
frameshift						0
inframe indel				3	2	5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	25	11	5

Variants in FOXF2

This is a list of pathogenic ClinVar variants found in the FOXF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-1389957-G-A		not specified	Uncertain significance (Sep 21, 2023)
6-1389960-G-A		not specified	Uncertain significance (Feb 13, 2024)
6-1389991-C-T		not specified	Uncertain significance (Aug 11, 2022)
6-1389999-C-A		not specified	Uncertain significance (Apr 26, 2023)
6-1390005-C-T		not specified	Uncertain significance (Mar 11, 2022)
6-1390024-C-T		not specified	Uncertain significance (Dec 14, 2023)
6-1390041-CCCG-C		FOXF2-related disorder	Benign (Aug 01, 2019)
6-1390041-CCCGCCGCCG-C		FOXF2-related disorder	Likely benign (Feb 09, 2024)
6-1390041-CCCGCCGCCGCCG-C		FOXF2-related disorder	Likely benign (Sep 01, 2022)
6-1390041-C-CCCG		FOXF2-related disorder	Benign (Sep 20, 2019)
6-1390068-G-T		FOXF2-related disorder	Likely benign (Feb 15, 2023)
6-1390073-G-A		FOXF2-related disorder	Likely benign (Sep 25, 2023)
6-1390074-G-C		not specified	Uncertain significance (Aug 14, 2023)
6-1390143-G-A		not specified • FOXF2-related disorder	Uncertain significance (May 12, 2024)
6-1390146-A-T		not specified	Uncertain significance (Aug 12, 2021)
6-1390150-C-T		FOXF2-related disorder	Likely benign (Aug 01, 2019)
6-1390178-C-T		FOXF2-related disorder	Likely benign (Apr 10, 2019)
6-1390187-C-T		FOXF2-related disorder	Likely benign (Jan 04, 2024)
6-1390207-G-A		not specified	Uncertain significance (Aug 12, 2021)
6-1390207-G-T		not specified	Uncertain significance (Mar 15, 2024)
6-1390299-A-T		not specified	Uncertain significance (Mar 30, 2024)
6-1390300-G-C		not specified	Uncertain significance (Mar 30, 2024)
6-1390322-G-A		FOXF2-related disorder	Likely benign (Sep 01, 2020)
6-1390365-G-T		not specified	Uncertain significance (Mar 30, 2024)
6-1390394-C-T		FOXF2-related disorder	Likely benign (May 22, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXF2	protein_coding	protein_coding	ENST00000259806	2	5764

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.847	0.153	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.853	172	206	0.833	0.00000990	2807
Missense in Polyphen		21	56.901	0.36906		587
Synonymous	-1.57	115	95.5	1.20	0.00000480	919
Loss of Function	2.72	1	10.5	0.0949	4.52e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000998	0.0000924
European (Non-Finnish)	0.0000713	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcription activator for a number of lung- specific genes.

Haploinsufficiency Scores

• pHI: 0.127
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxf2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; vision/eye phenotype; craniofacial phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: foxf2b
• Affected structure: pericyte
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: epithelial to mesenchymal transition;extracellular matrix organization;establishment of planar polarity of embryonic epithelium;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;embryonic digestive tract development;embryonic camera-type eye morphogenesis;genitalia development;roof of mouth development
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription factor binding;sequence-specific DNA binding