FER

FER tyrosine kinase, the group of Fes family tyrosine kinases|Protein phosphatase 1 regulatory subunits|SH2 domain containing|F-BAR domain containing

Basic information

Region (hg38): 5:108747840-109196841

Links

ENSG00000151422 ∙ NCBI:2241 ∙ OMIM:176942 ∙ HGNC:3655 ∙ Uniprot:P16591 ∙ 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 FER gene.

• Inborn genetic diseases (20 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FER 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	3	4
missense			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	20	2	5

Variants in FER

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

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

Position	Type	Phenotype	Significance	ClinVar
5-108798234-C-A		not specified	Uncertain significance (Oct 24, 2023)
5-108798237-G-C		not specified	Uncertain significance (May 17, 2023)
5-108798371-T-C			Benign (Jul 13, 2018)
5-108832819-A-G		not specified	Uncertain significance (Aug 16, 2021)
5-108832867-T-C		not specified	Uncertain significance (Jul 05, 2023)
5-108832885-A-G		not specified	Uncertain significance (Jun 28, 2022)
5-108832908-G-C		not specified	Uncertain significance (Nov 02, 2023)
5-108867763-T-TC			Benign (Dec 31, 2019)
5-108867811-A-G		not specified	Uncertain significance (Feb 05, 2024)
5-108871372-A-G		not specified	Uncertain significance (Feb 11, 2022)
5-108871399-A-C		not specified	Uncertain significance (Nov 17, 2022)
5-108871481-A-G		not specified	Uncertain significance (Mar 25, 2022)
5-108872103-G-A		not specified	Uncertain significance (May 17, 2023)
5-108872211-A-G		not specified	Uncertain significance (Jan 31, 2023)
5-108883422-T-C		not specified	Uncertain significance (Feb 13, 2024)
5-108883500-C-T		not specified	Uncertain significance (Feb 10, 2022)
5-108897661-T-C			Benign (Dec 31, 2019)
5-108897834-T-A		not specified	Uncertain significance (Jul 13, 2022)
5-108946144-G-T		not specified	Uncertain significance (May 17, 2023)
5-108954774-G-A		not specified	Uncertain significance (Jan 23, 2024)
5-108954844-T-G		not specified	Uncertain significance (Feb 28, 2023)
5-108954888-T-C		not specified	Uncertain significance (Nov 27, 2023)
5-108954928-T-G		not specified	Uncertain significance (Feb 10, 2023)
5-108959248-T-C			Benign (Dec 31, 2019)
5-108959273-A-C		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FER	protein_coding	protein_coding	ENST00000281092	18	449020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.663	0.337	125703	0	32	125735	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	339	411	0.825	0.0000198	5442
Missense in Polyphen		115	168.26	0.68346		2180
Synonymous	-0.749	152	141	1.08	0.00000719	1410
Loss of Function	5.04	10	47.5	0.211	0.00000235	612

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000411	0.000398
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.000113	0.000109
South Asian	0.0000329	0.0000327
Other	0.000215	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine-protein kinase that acts downstream of cell surface receptors for growth factors and plays a role in the regulation of the actin cytoskeleton, microtubule assembly, lamellipodia formation, cell adhesion, cell migration and chemotaxis. Acts downstream of EGFR, KIT, PDGFRA and PDGFRB. Acts downstream of EGFR to promote activation of NF-kappa-B and cell proliferation. May play a role in the regulation of the mitotic cell cycle. Plays a role in the insulin receptor signaling pathway and in activation of phosphatidylinositol 3-kinase. Acts downstream of the activated FCER1 receptor and plays a role in FCER1 (high affinity immunoglobulin epsilon receptor)-mediated signaling in mast cells. Plays a role in the regulation of mast cell degranulation. Plays a role in leukocyte recruitment and diapedesis in response to bacterial lipopolysaccharide (LPS). Plays a role in synapse organization, trafficking of synaptic vesicles, the generation of excitatory postsynaptic currents and neuron-neuron synaptic transmission. Plays a role in neuronal cell death after brain damage. Phosphorylates CTTN, CTNND1, PTK2/FAK1, GAB1, PECAM1 and PTPN11. May phosphorylate JUP and PTPN1. Can phosphorylate STAT3, but the biological relevance of this depends on cell type and stimulus. {ECO:0000269|PubMed:12972546, ECO:0000269|PubMed:14517306, ECO:0000269|PubMed:19147545, ECO:0000269|PubMed:19339212, ECO:0000269|PubMed:19738202, ECO:0000269|PubMed:20111072, ECO:0000269|PubMed:21518868, ECO:0000269|PubMed:22223638, ECO:0000269|PubMed:7623846, ECO:0000269|PubMed:9722593}.
• Pathway: Adherens junction - Homo sapiens (human);Signal Transduction;TCR;Signaling by SCF-KIT;Signaling by Receptor Tyrosine Kinases;Fc-epsilon receptor I signaling in mast cells;N-cadherin signaling events;Signaling events mediated by Stem cell factor receptor (c-Kit);Signaling events mediated by PTP1B (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.254
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.6

Haploinsufficiency Scores

• pHI: 0.104
• hipred: Y
• hipred_score: 0.756
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.787

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fer
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: fer
• Affected structure: ceratohyal cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: microtubule cytoskeleton organization;mitotic cell cycle;regulation of protein phosphorylation;protein phosphorylation;chemotaxis;cell adhesion;tyrosine phosphorylation of STAT protein;cell population proliferation;positive regulation of cell population proliferation;regulation of lamellipodium assembly;regulation of fibroblast migration;peptidyl-tyrosine phosphorylation;cytokine-mediated signaling pathway;positive regulation of cell migration;positive regulation of actin filament polymerization;actin cytoskeleton reorganization;response to lipopolysaccharide;cellular response to insulin stimulus;negative regulation of mast cell activation involved in immune response;substrate adhesion-dependent cell spreading;cellular response to reactive oxygen species;extracellular matrix-cell signaling;intracellular signal transduction;cellular response to macrophage colony-stimulating factor stimulus;response to platelet-derived growth factor;insulin receptor signaling pathway via phosphatidylinositol 3-kinase;Fc-epsilon receptor signaling pathway;Kit signaling pathway;regulation of epidermal growth factor receptor signaling pathway;regulation of cell population proliferation;regulation of mast cell degranulation;cell-cell adhesion mediated by cadherin;protein autophosphorylation;platelet-derived growth factor receptor signaling pathway;diapedesis;positive regulation of NF-kappaB transcription factor activity;interleukin-6-mediated signaling pathway
• Cellular component: nuclear chromatin;nucleus;cytoplasm;cytosol;cell cortex;actin cytoskeleton;microtubule cytoskeleton;lamellipodium;cell junction;extrinsic component of cytoplasmic side of plasma membrane
• Molecular function: protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;epidermal growth factor receptor binding;protein binding;ATP binding;protein phosphatase 1 binding;lipid binding