FGF6

fibroblast growth factor 6, the group of Receptor ligands|Fibroblast growth factor family

Basic information

Region (hg38): 12:4428155-4445815

Links

ENSG00000111241 ∙ NCBI:2251 ∙ OMIM:134921 ∙ HGNC:3684 ∙ Uniprot:P10767 ∙ 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 FGF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGF6 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				1		1
missense			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	1

Variants in FGF6

This is a list of pathogenic ClinVar variants found in the FGF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-4434252-G-T		not specified	Uncertain significance (Aug 12, 2024)
12-4434271-G-A		not specified	Uncertain significance (Jan 09, 2024)
12-4434283-C-T		not specified	Uncertain significance (Jan 31, 2025)
12-4434321-T-A			Benign (Oct 16, 2019)
12-4434321-T-C		not specified	Uncertain significance (Jul 02, 2024)
12-4434328-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-4434357-G-A		not specified	Uncertain significance (Aug 05, 2024)
12-4444135-T-G		not specified	Uncertain significance (Jan 17, 2024)
12-4444139-G-A		not specified	Likely benign (Dec 06, 2023)
12-4444165-C-A		not specified	Uncertain significance (May 24, 2024)
12-4444165-C-T		not specified	Uncertain significance (Nov 21, 2024)
12-4444168-C-T		not specified	Likely benign (Oct 03, 2023)
12-4444216-C-T		not specified	Uncertain significance (Jul 11, 2023)
12-4444225-T-C		not specified	Uncertain significance (Oct 18, 2021)
12-4444235-G-T		not specified	Uncertain significance (Jun 03, 2024)
12-4445261-C-T		not specified	Uncertain significance (Nov 09, 2024)
12-4445280-G-T		not specified	Uncertain significance (Dec 27, 2023)
12-4445306-A-G		not specified	Uncertain significance (Apr 12, 2024)
12-4445381-C-T		not specified	Uncertain significance (Nov 15, 2023)
12-4445404-G-T		not specified	Uncertain significance (Feb 24, 2025)
12-4445443-C-T		not specified	Uncertain significance (Jun 19, 2024)
12-4445452-G-A		not specified	Uncertain significance (Jun 07, 2023)
12-4445465-C-T		not specified	Uncertain significance (Jan 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGF6	protein_coding	protein_coding	ENST00000228837	3	17460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000398	0.650	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.434	117	131	0.893	0.00000842	1302
Missense in Polyphen		44	54.434	0.80832		606
Synonymous	-1.30	72	59.3	1.22	0.00000398	450
Loss of Function	0.719	6	8.22	0.730	4.35e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000479	0.0000462
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000665	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in the regulation of cell proliferation, cell differentiation, angiogenesis and myogenesis, and is required for normal muscle regeneration. {ECO:0000269|PubMed:8663044}.
• 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);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;Phospholipase C-mediated cascade; FGFR2;SHC-mediated cascade:FGFR2;PI-3K cascade:FGFR2;Downstream signaling of activated FGFR2;PI-3K cascade:FGFR4;Disease;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;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;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 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);Syndecan-4-mediated signaling events;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; FGFR4 (Consensus)

Recessive Scores

• pRec: 0.198

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.697
• hipred: Y
• hipred_score: 0.765
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgf6
• Phenotype: cellular phenotype; craniofacial phenotype; muscle phenotype; growth/size/body region phenotype; 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); skeleton phenotype; normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: MAPK cascade;cartilage condensation;angiogenesis;signal transduction;cell-cell signaling;cell population proliferation;positive regulation of cell population proliferation;fibroblast growth factor receptor signaling pathway;regulation of signaling receptor activity;peptidyl-tyrosine phosphorylation;phosphatidylinositol-3-phosphate biosynthetic process;myoblast differentiation;phosphatidylinositol phosphorylation;positive regulation of cell division;positive regulation of protein kinase B signaling
• Cellular component: extracellular region;extracellular space;sarcolemma
• Molecular function: protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;fibroblast growth factor receptor binding;growth factor activity;1-phosphatidylinositol-3-kinase activity;phosphatidylinositol-4,5-bisphosphate 3-kinase activity