FRS3

fibroblast growth factor receptor substrate 3

Basic information

Region (hg38): 6:41770176-41786542

Links

ENSG00000137218 ∙ NCBI:10817 ∙ OMIM:607744 ∙ HGNC:16970 ∙ Uniprot:O43559 ∙ 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 FRS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRS3 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			47	1	2	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	1	2

Variants in FRS3

This is a list of pathogenic ClinVar variants found in the FRS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-41770633-C-T		not specified	Uncertain significance (Feb 24, 2022)
6-41770670-G-C		not specified	Uncertain significance (May 29, 2024)
6-41770776-G-A		not specified	Uncertain significance (Jan 10, 2023)
6-41770839-A-G		not specified	Uncertain significance (May 08, 2023)
6-41770878-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-41770882-G-A		not specified	Uncertain significance (Nov 15, 2024)
6-41770902-A-G		not specified	Uncertain significance (Jul 14, 2024)
6-41770906-T-C		not specified	Uncertain significance (Apr 25, 2023)
6-41770917-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-41770921-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-41770969-G-A		not specified	Uncertain significance (Nov 13, 2024)
6-41771052-G-A		not specified	Uncertain significance (Aug 12, 2021)
6-41771056-C-T		not specified	Uncertain significance (May 30, 2024)
6-41771065-C-T		not specified	Uncertain significance (Jun 29, 2022)
6-41771092-C-T		not specified	Uncertain significance (Dec 10, 2024)
6-41771107-C-A		not specified	Uncertain significance (Aug 20, 2023)
6-41771125-G-C		not specified	Uncertain significance (Jan 08, 2024)
6-41771178-G-A		not specified	Uncertain significance (Aug 11, 2024)
6-41771190-C-A		not specified	Uncertain significance (Aug 04, 2023)
6-41771211-C-T		not specified	Uncertain significance (Aug 15, 2023)
6-41771220-C-T		not specified	Uncertain significance (Dec 05, 2022)
6-41771275-C-A		not specified	Uncertain significance (Sep 04, 2024)
6-41771283-T-C		not specified	Uncertain significance (Apr 17, 2023)
6-41771284-T-C		not specified	Uncertain significance (Dec 09, 2024)
6-41771285-A-T		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRS3	protein_coding	protein_coding	ENST00000373018	5	16367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.550	0.449	125727	0	7	125734	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.916	276	322	0.856	0.0000210	3176
Missense in Polyphen		69	108.23	0.63753		1137
Synonymous	-0.884	144	131	1.10	0.00000795	1041
Loss of Function	3.28	4	19.7	0.203	0.00000125	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000475	0.0000462
European (Non-Finnish)	0.0000270	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein that links FGF and NGF receptors to downstream signaling pathways. Involved in the activation of MAP kinases. Down-regulates ERK2 signaling by interfering with the phosphorylation and nuclear translocation of ERK2. {ECO:0000269|PubMed:15094036}.
• Pathway: Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;FRS-mediated FGFR2 signaling;Signaling by FGFR2;FRS-mediated FGFR3 signaling;Downstream signaling of activated FGFR2;Downstream signaling of activated FGFR3;Signaling by FGFR3;Signal Transduction;FRS-mediated FGFR4 signaling;Downstream signaling of activated FGFR4;Signaling by FGFR4;Signaling by FGFR;FGF;Signaling by NTRK2 (TRKB);Signaling by NTRKs;BDNF;EGFR1;SHP2 signaling;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Activated NTRK2 signals through FRS2 and FRS3;Signaling by Receptor Tyrosine Kinases;Neurotrophic factor-mediated Trk receptor signaling;Downstream signaling of activated FGFR1;FRS-mediated FGFR1 signaling;Signaling by FGFR1 (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.440
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.57

Haploinsufficiency Scores

• pHI: 0.958
• hipred: Y
• hipred_score: 0.825
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frs3
• Phenotype: cellular phenotype; craniofacial 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); vision/eye phenotype

Gene ontology

• Biological process: MAPK cascade;signal transduction;fibroblast growth factor receptor signaling pathway
• Cellular component: plasma membrane
• Molecular function: Ras guanyl-nucleotide exchange factor activity;fibroblast growth factor receptor binding;protein binding;identical protein binding