GeneBe

FGF12

fibroblast growth factor 12, the group of Fibroblast growth factor family

Basic information

Region (hg38): 3:192139390-192767764

Previous symbols: [ "FGF12B" ]

Links

ENSG00000114279 ∙ NCBI:2257 ∙ OMIM:601513 ∙ HGNC:3668 ∙ Uniprot:P61328 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • developmental and epileptic encephalopathy, 47 (Moderate), mode of inheritance: AD
  • undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
  • developmental and epileptic encephalopathy, 47 (Strong), mode of inheritance: AD
  • genetic developmental and epileptic encephalopathy (Definitive), mode of inheritance: AD
  • developmental and epileptic encephalopathy, 47 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Developmental and epileptic encephalopathy 47ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic27164707

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FGF12 gene.

  • not_provided (199 variants)
  • Developmental_and_epileptic_encephalopathy,_47 (15 variants)
  • Inborn_genetic_diseases (15 variants)
  • FGF12-related_disorder (7 variants)
  • Seizure (1 variants)
  • Early_onset_epileptic_encephalopathy (1 variants)
  • Gestational_diabetes_mellitus_uncontrolled (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGF12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004113.6. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
25
clinvar
2
clinvar
 27
missense
1
clinvar
2
clinvar
54
clinvar
13
clinvar
7
clinvar
 77
nonsense
2
clinvar
 2
start loss
0
frameshift
1
clinvar
2
clinvar
 3
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 1 3 59 38 9
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FGF12protein_codingprotein_codingENST00000454309 5628370
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.6230.376125742041257460.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.52911420.6400.000007181571
Missense in Polyphen1646.3890.34491528
Synonymous0.4535054.20.9220.00000279478
Loss of Function2.63211.70.1715.83e-7141

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.000009280.00000879
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in nervous system development and function. Involved in the positive regulation of voltage-gated sodium channel activity. Promotes neuronal excitability by elevating the voltage dependence of neuronal sodium channel SCN8A fast inactivation. {ECO:0000269|PubMed:27164707}.;
Pathway
MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;Phase 0 - rapid depolarisation;Cardiac conduction;Muscle contraction (Consensus)

Recessive Scores

pRec
0.174

Intolerance Scores

loftool
0.209
rvis_EVS
-0.16
rvis_percentile_EVS
41.25

Haploinsufficiency Scores

pHI
0.908
hipred
Y
hipred_score
0.697
ghis
0.563

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.731

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Fgf12
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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
regulation of membrane depolarization;signal transduction;cell-cell signaling;chemical synaptic transmission;nervous system development;heart development;adult locomotory behavior;fibroblast growth factor receptor signaling pathway;regulation of signaling receptor activity;positive regulation of sodium ion transport;neuromuscular process;cardiac muscle cell action potential involved in contraction;regulation of neuronal action potential;regulation of sodium ion transmembrane transport;regulation of voltage-gated sodium channel activity;regulation of sodium ion transmembrane transporter activity;negative regulation of cation channel activity
Cellular component
extracellular space;nucleus
Molecular function
protein binding;growth factor activity;sodium channel regulator activity;ion channel binding