FRK

fyn related Src family tyrosine kinase, the group of Src family tyrosine kinases|SH2 domain containing

Basic information

Region (hg38): 6:115931148-116060891

Previous symbols: [ "PTK5" ]

Links

ENSG00000111816 ∙ NCBI:2444 ∙ OMIM:606573 ∙ HGNC:3955 ∙ Uniprot:P42685 ∙ 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 FRK gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRK 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						0
missense			16			16
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in FRK

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

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

Position	Type	Phenotype	Significance	ClinVar
6-115942446-A-G		not specified	Uncertain significance (Aug 02, 2021)
6-115943046-A-G		not specified	Uncertain significance (Apr 05, 2023)
6-115943073-G-C			Uncertain significance (Jan 30, 2023)
6-115943103-T-C		not specified	Uncertain significance (Sep 17, 2021)
6-115943109-C-T		not specified	Uncertain significance (Jul 11, 2023)
6-115943119-C-T		not specified	Uncertain significance (Feb 17, 2024)
6-115944330-G-T		not specified	Uncertain significance (Aug 12, 2021)
6-115944414-A-G		not specified	Uncertain significance (Jun 01, 2022)
6-115967662-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-115968677-G-T		not specified	Uncertain significance (Dec 17, 2023)
6-115968722-C-T		Hemifacial microsomia	Uncertain significance (May 10, 2021)
6-115968725-C-T		not specified	Uncertain significance (May 16, 2022)
6-115968728-C-A		not specified	Uncertain significance (Jan 23, 2024)
6-116003887-G-C		not specified	Uncertain significance (May 09, 2022)
6-116003916-T-C		not specified	Uncertain significance (Mar 24, 2023)
6-116003927-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-116003931-C-T		not specified	Uncertain significance (Mar 24, 2023)
6-116003934-T-A		not specified	Uncertain significance (Dec 21, 2021)
6-116060097-A-G		not specified	Uncertain significance (Feb 16, 2023)
6-116060186-C-A		not specified	Uncertain significance (May 05, 2023)
6-116060250-G-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRK	protein_coding	protein_coding	ENST00000606080	8	129610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-12	0.363	125627	1	120	125748	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.686	239	271	0.883	0.0000141	3304
Missense in Polyphen		78	114.77	0.67964		1361
Synonymous	-0.857	114	103	1.11	0.00000594	937
Loss of Function	1.20	22	29.0	0.759	0.00000178	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00103
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000423	0.000396
Middle Eastern	0.000218	0.000217
South Asian	0.00142	0.00141
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-receptor tyrosine-protein kinase that negatively regulates cell proliferation. Positively regulates PTEN protein stability through phosphorylation of PTEN on 'Tyr-336', which in turn prevents its ubiquitination and degradation, possibly by reducing its binding to NEDD4. May function as a tumor suppressor. {ECO:0000269|PubMed:19345329}.
• Pathway: Neutrophil degranulation;Signal Transduction;Regulation of PTEN stability and activity;Innate Immune System;Immune System;EGFR1;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.458
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.74

Haploinsufficiency Scores

• pHI: 0.653
• hipred: N
• hipred_score: 0.251
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.951

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frk
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;protein phosphorylation;transmembrane receptor protein tyrosine kinase signaling pathway;negative regulation of cell population proliferation;cell differentiation;peptidyl-tyrosine autophosphorylation;neutrophil degranulation
• Cellular component: extracellular region;nucleus;cytosol;extrinsic component of cytoplasmic side of plasma membrane;azurophil granule lumen;specific granule lumen;extracellular exosome
• Molecular function: protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;signaling receptor binding;protein binding;ATP binding