FGF20

fibroblast growth factor 20, the group of Fibroblast growth factor family

Basic information

Region (hg38): 8:16992180-17002345

Links

ENSG00000078579 ∙ NCBI:26281 ∙ OMIM:605558 ∙ HGNC:3677 ∙ Uniprot:Q9NP95 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• bilateral renal agenesis (Supportive), mode of inheritance: AR
• renal hypodysplasia/aplasia 2 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Renal hypodysplasia/aplasia 2	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Renal	22698282

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FGF20 gene.

• not provided (35 variants)
• Inborn genetic diseases (16 variants)
• Renal hypodysplasia/aplasia 2 (2 variants)
• Parkinson disease, late-onset (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGF20 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				7	4	11
missense			24	1	3	28
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding					11	11
Total	0	1	25	8	18

Variants in FGF20

This is a list of pathogenic ClinVar variants found in the FGF20 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-16992890-G-A		Parkinson disease, late-onset	Benign (Jun 19, 2021)
8-16992907-A-G			Benign (Jun 18, 2021)
8-16992989-C-G			Benign (Nov 11, 2018)
8-16993078-G-A			Likely benign (Dec 22, 2023)
8-16993085-A-G		not specified	Uncertain significance (Jan 17, 2023)
8-16993092-C-A			Uncertain significance (Jul 05, 2022)
8-16993092-C-T			Benign (Jan 19, 2024)
8-16993098-A-G		not specified	Uncertain significance (Sep 27, 2022)
8-16993125-C-G		not specified	Uncertain significance (Jun 24, 2022)
8-16993162-C-G			Uncertain significance (Aug 10, 2023)
8-16993173-C-A			Uncertain significance (Jun 14, 2023)
8-16993174-G-A		FGF20-related disorder	Likely benign (Apr 20, 2020)
8-16993185-G-C			Benign (Jul 17, 2023)
8-16993204-T-G			Likely benign (Sep 06, 2023)
8-16993239-T-C		not specified	Uncertain significance (Mar 02, 2023)
8-16993242-A-G		not specified	Uncertain significance (Jan 26, 2022)
8-16993244-A-G		not specified	Uncertain significance (Feb 06, 2023)
8-16993261-G-C		not specified	Uncertain significance (Oct 29, 2021)
8-16993296-T-C			Uncertain significance (Sep 19, 2023)
8-16993311-G-C		not specified	Uncertain significance (Jan 16, 2024)
8-16993315-C-G			Uncertain significance (Jul 22, 2023)
8-16993318-C-T		Renal hypodysplasia/aplasia 2	Likely pathogenic (May 28, 2019)
8-16993331-G-C			Likely benign (Mar 22, 2023)
8-16993369-T-G			Benign (Jun 20, 2021)
8-16993428-G-T			Benign (Jun 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGF20	protein_coding	protein_coding	ENST00000180166	3	10013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.814	0.182	123721	0	3	123724	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.874	121	96.8	1.25	0.00000468	1299
Missense in Polyphen		39	38.934	1.0017		457
Synonymous	-1.46	51	39.3	1.30	0.00000199	414
Loss of Function	2.18	0	5.55	0.00	2.30e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neurotrophic factor that regulates central nervous development and function. {ECO:0000269|PubMed:16597617}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Melanoma - Homo sapiens (human);Breast cancer - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hair Follicle Development- Induction (Part 1 of 3);MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;FGFR2c ligand binding and activation;FGFR2 ligand binding and activation;FRS-mediated FGFR2 signaling;Negative regulation of FGFR2 signaling;Signaling by FGFR2;FGFR3b ligand binding and activation;Phospholipase C-mediated cascade; FGFR2;FGFR3c ligand binding and activation;SHC-mediated cascade:FGFR2;FRS-mediated FGFR3 signaling;PI-3K cascade:FGFR2;Downstream signaling of activated FGFR2;SHC-mediated cascade:FGFR3;PI-3K cascade:FGFR4;PI-3K cascade:FGFR3;Downstream signaling of activated FGFR3;Disease;Negative regulation of FGFR3 signaling;Signaling by FGFR3;FGFR4 ligand binding and activation;Signal Transduction;FRS-mediated FGFR4 signaling;SHC-mediated cascade:FGFR4;Downstream signaling of activated FGFR4;Negative regulation of FGFR4 signaling;Signaling by FGFR4;Signaling by FGFR;FGFR3 ligand binding and activation;FGFR3 mutant receptor activation;PI3K Cascade;IRS-mediated signalling;Insulin receptor signalling cascade;Activated point mutants of FGFR2;Signaling by Insulin receptor;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;FGF;Signaling by FGFR2 in disease;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Signaling by activated point mutants of FGFR3;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;PIP3 activates AKT signaling;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;FGFR2 mutant receptor activation;Signaling by FGFR3 point mutants in cancer;Signaling by FGFR3 in disease;Signaling by FGFR in disease;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;GPCR signaling-G alpha i;IRS-related events triggered by IGF1R;IGF1R signaling cascade;Signaling by activated point mutants of FGFR1;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Signaling by Receptor Tyrosine Kinases;Intracellular signaling by second messengers;Phospholipase C-mediated cascade: FGFR1;Diseases of signal transduction;Downstream signaling of activated FGFR1;Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R);FGFR1c ligand binding and activation;FGFR1 ligand binding and activation;FRS-mediated FGFR1 signaling;SHC-mediated cascade:FGFR1;PI-3K cascade:FGFR1;Negative regulation of FGFR1 signaling;Signaling by FGFR1;Phospholipase C-mediated cascade; FGFR3;Phospholipase C-mediated cascade; FGFR4 (Consensus)

Recessive Scores

• pRec: 0.230

Haploinsufficiency Scores

• pHI: 0.729
• hipred: Y
• hipred_score: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.343

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgf20
• Phenotype: hearing/vestibular/ear 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: fgf20b
• Affected structure: pharyngeal arch cartilage
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: MAPK cascade;signal transduction;cell-cell signaling;positive regulation of cell population proliferation;fibroblast growth factor receptor signaling pathway;regulation of signaling receptor activity;regulation of dopamine secretion;peptidyl-tyrosine phosphorylation;phosphatidylinositol-3-phosphate biosynthetic process;negative regulation of neuron apoptotic process;phosphatidylinositol phosphorylation;positive regulation of protein kinase B signaling;regulation of cardiac muscle cell proliferation;inner ear receptor cell differentiation;positive regulation of ERK1 and ERK2 cascade;positive regulation of dopaminergic neuron differentiation
• Cellular component: extracellular region
• Molecular function: protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;signaling receptor binding;fibroblast growth factor receptor binding;growth factor activity;1-phosphatidylinositol-3-kinase activity;heparan sulfate proteoglycan binding;phosphatidylinositol-4,5-bisphosphate 3-kinase activity;receptor-receptor interaction