FGFR1OP2

FGFR1 oncogene partner 2, the group of STRIPAK complex

Basic information

Region (hg38): 12:26938469-26966650

Links

ENSG00000111790 ∙ NCBI:26127 ∙ OMIM:608858 ∙ HGNC:23098 ∙ Uniprot:Q9NVK5 ∙ 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 FGFR1OP2 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGFR1OP2 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in FGFR1OP2

This is a list of pathogenic ClinVar variants found in the FGFR1OP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-26954274-G-A		not specified	Uncertain significance (Jul 15, 2021)
12-26956572-A-C		not specified	Uncertain significance (Dec 19, 2022)
12-26956585-C-T		not specified	Uncertain significance (Apr 13, 2022)
12-26957688-C-G		not specified	Uncertain significance (Aug 12, 2021)
12-26957706-C-T		not specified	Uncertain significance (Jul 25, 2023)
12-26960528-A-C		not specified	Uncertain significance (Feb 15, 2023)
12-26963366-A-G		not specified	Uncertain significance (Oct 04, 2022)
12-26963406-T-C		not specified	Uncertain significance (Jun 13, 2023)
12-26964669-C-T		not specified	Likely benign (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGFR1OP2	protein_coding	protein_coding	ENST00000229395	6	28268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000496	0.972	125727	0	18	125745	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	108	143	0.755	0.00000802	1684
Missense in Polyphen		33	46.631	0.70768		590
Synonymous	0.200	50	51.8	0.965	0.00000329	449
Loss of Function	1.95	8	16.6	0.483	0.00000110	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000222	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000716	0.0000703
Middle Eastern	0.000222	0.000217
South Asian	0.0000340	0.0000327
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in wound healing pathway. {ECO:0000250}.
• Pathway: VEGF Signaling Pathway;Disease;Signaling by FGFR in disease;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.153
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.166
• hipred: Y
• hipred_score: 0.775
• ghis: 0.675

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgfr1op2

Gene ontology

• Biological process: peptidyl-tyrosine phosphorylation;wound healing
• Cellular component: cytosol
• Molecular function: protein tyrosine kinase activity;protein binding;protein homodimerization activity