FGF13

fibroblast growth factor 13, the group of Fibroblast growth factor family|MicroRNA protein coding host genes

Basic information

Region (hg38): X:138614726-139222777

Previous symbols: [ "LINC00889" ]

Links

ENSG00000129682 ∙ NCBI:2258 ∙ OMIM:300070 ∙ HGNC:3670 ∙ Uniprot:Q92913 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
• developmental and epileptic encephalopathy, 90 (Moderate), mode of inheritance: XL
• developmental and epileptic encephalopathy, 90 (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 90; Intellectual developmental disorder, X-linked 110	XL	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	Neurologic	33245860; 34184986

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FGF13 gene.

• not provided (16 variants)
• Developmental and epileptic encephalopathy, 90 (4 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGF13 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	1	3
missense		1	12	2		15
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	1	1	14	4	1

Variants in FGF13

This is a list of pathogenic ClinVar variants found in the FGF13 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-138623650-G-A			Uncertain significance (Apr 20, 2022)
X-138632868-G-T			Uncertain significance (Jun 10, 2022)
X-138632886-G-A			Likely benign (May 01, 2023)
X-138632894-C-T		not specified	Uncertain significance (Jan 22, 2024)
X-138632895-G-A			Benign (Oct 09, 2018)
X-138632900-A-G			Likely benign (May 18, 2018)
X-138635466-G-A		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
X-138635469-T-G		FGF13-related disorder	Likely benign (Mar 20, 2023)
X-138635531-T-C			Uncertain significance (Jan 02, 2022)
X-138703001-C-T			Uncertain significance (Feb 14, 2022)
X-138708823-G-A			Uncertain significance (Feb 14, 2023)
X-138708827-T-C			Uncertain significance (Aug 29, 2022)
X-138708860-C-T		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
X-138710845-G-T			Likely benign (Jul 11, 2018)
X-138710877-A-C		Developmental and epileptic encephalopathy, 90	Uncertain significance (-)
X-138710903-C-G			Uncertain significance (Aug 23, 2022)
X-138710963-C-G		Developmental and epileptic encephalopathy, 90	Pathogenic (Feb 19, 2021)
X-138710972-C-G		Developmental and epileptic encephalopathy, 90	Pathogenic (Feb 19, 2021)
X-138710972-C-T		Neurodevelopmental disorder	Uncertain significance (Jan 19, 2021)
X-138710973-G-A		Developmental and epileptic encephalopathy, 90	Pathogenic (Feb 19, 2021)
X-138710981-G-T		Developmental and epileptic encephalopathy, 90	Pathogenic (Jun 28, 2022)
X-138710990-A-C		Developmental and epileptic encephalopathy, 90	Likely pathogenic (Jul 24, 2021)
X-138710999-G-C		Developmental and epileptic encephalopathy, 90	Likely pathogenic (-)
X-138710999-G-T			Uncertain significance (Mar 02, 2023)
X-138739247-T-C		FGF13-related disorder	Likely benign (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGF13	protein_coding	protein_coding	ENST00000370603	6	591205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.895	0.105	124263	1	3	124267	0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	55	99.7	0.552	0.00000778	1653
Missense in Polyphen		9	24.672	0.36479		436
Synonymous	0.420	38	41.4	0.917	0.00000354	482
Loss of Function	2.90	1	11.7	0.0855	0.00000103	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000411	0.0000411
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000398	0.0000266
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-binding protein which directly binds tubulin and is involved in both polymerization and stabilization of microtubules. Through its action on microtubules, may participate to the refinement of axons by negatively regulating axonal and leading processes branching. Plays a crucial role in neuron polarization and migration in the cerebral cortex and the hippocampus. {ECO:0000269|PubMed:15282281}.; FUNCTION: May also play a role in MAPK signaling. {ECO:0000269|PubMed:15282281}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;MAPK Signaling Pathway;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;FGF;GPCR signaling-G alpha s Epac and ERK;Phase 0 - rapid depolarisation;Cardiac conduction;Muscle contraction;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.226
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.897
• hipred: Y
• hipred_score: 0.702
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Fgf13
• Phenotype: cellular 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); 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)

Gene ontology

• Biological process: MAPK cascade;neuron migration;sodium ion transport;negative regulation of microtubule depolymerization;signal transduction;cell-cell signaling;nervous system development;learning;memory;regulation of signaling receptor activity;hippocampus development;cerebral cortex cell migration;activation of protein kinase activity;establishment of neuroblast polarity;microtubule polymerization;negative regulation of collateral sprouting;protein localization to plasma membrane;regulation of cardiac muscle cell action potential involved in regulation of contraction
• Cellular component: extracellular region;nucleus;nucleolus;cytoplasm;cytosol;microtubule;plasma membrane;intercalated disc;lateral plasma membrane;filopodium;axon;dendrite;growth cone;neuron projection
• Molecular function: protein binding;microtubule binding;growth factor activity;sodium channel regulator activity;protein kinase activator activity;ion channel binding;beta-tubulin binding