FARP2

FERM, ARH/RhoGEF and pleckstrin domain protein 2, the group of Dbl family Rho GEFs|FERM domain containing|Pleckstrin homology domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:241356285-241494841

Links

ENSG00000006607 ∙ NCBI:9855 ∙ OMIM:617586 ∙ HGNC:16460 ∙ Uniprot:O94887 ∙ 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 FARP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FARP2 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				10	2	12
missense			84	13	5	102
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding						0
Total	0	0	84	23	7

Variants in FARP2

This is a list of pathogenic ClinVar variants found in the FARP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-241373128-A-C			Benign/Likely benign (Apr 01, 2022)
2-241373156-C-T		not specified	Uncertain significance (Jun 30, 2023)
2-241373159-T-G		not specified	Uncertain significance (Jun 11, 2021)
2-241373178-T-C			Likely benign (Apr 24, 2018)
2-241373187-G-A		not specified	Uncertain significance (May 09, 2023)
2-241373202-G-A			Likely benign (Feb 09, 2018)
2-241373240-C-T			Likely benign (Feb 01, 2023)
2-241373241-A-G			Benign (Apr 23, 2018)
2-241403831-A-G		not specified	Uncertain significance (May 14, 2024)
2-241403882-G-A		not specified	Likely benign (Feb 02, 2022)
2-241403895-A-G		not specified	Uncertain significance (Dec 08, 2023)
2-241403921-C-G			Likely benign (Aug 15, 2018)
2-241403930-T-A		not specified	Uncertain significance (Aug 02, 2021)
2-241413302-C-G			Benign (Aug 08, 2018)
2-241413332-G-A			Likely benign (Apr 19, 2018)
2-241413340-G-A		not specified	Uncertain significance (Aug 17, 2022)
2-241413360-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-241413369-C-G		not specified	Uncertain significance (May 09, 2024)
2-241413370-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-241418067-G-T		not specified	Uncertain significance (Apr 15, 2024)
2-241418095-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-241431695-A-G		not specified	Uncertain significance (Jan 12, 2024)
2-241431701-T-C			Likely benign (Aug 15, 2018)
2-241434192-G-A		not specified	Uncertain significance (Apr 28, 2022)
2-241434195-G-C		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FARP2	protein_coding	protein_coding	ENST00000264042	26	138599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.64e-36	0.0000263	125462	0	286	125748	0.00114

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.331	639	616	1.04	0.0000372	6872
Missense in Polyphen		250	246.42	1.0145		3009
Synonymous	-0.336	254	247	1.03	0.0000157	2057
Loss of Function	0.377	56	59.1	0.947	0.00000304	665

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00193
Ashkenazi Jewish	0.000601	0.000595
East Asian	0.00268	0.00267
Finnish	0.000278	0.000277
European (Non-Finnish)	0.00119	0.00117
Middle Eastern	0.00268	0.00267
South Asian	0.00111	0.00105
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as guanine nucleotide exchange factor that activates RAC1. May have relatively low activity. Plays a role in the response to class 3 semaphorins and remodeling of the actin cytoskeleton. Plays a role in TNFSF11-mediated osteoclast differentiation, especially in podosome rearrangement and reorganization of the actin cytoskeleton. Regulates the activation of ITGB3, integrin signaling and cell adhesion (By similarity). {ECO:0000250}.
• Pathway: Adherens junction - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Developmental Biology;SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion;Semaphorin interactions;Axon guidance;Regulation of CDC42 activity;Nectin adhesion pathway (Consensus)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.735
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.31

Haploinsufficiency Scores

• pHI: 0.0777
• hipred: Y
• hipred_score: 0.503
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Farp2
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;neuron remodeling;Rac protein signal transduction;hair cycle process;osteoclast differentiation;actin cytoskeleton reorganization;regulation of integrin activation;regulation of Rho protein signal transduction;semaphorin-plexin signaling pathway;podosome assembly
• Cellular component: cytoplasm;cytosol;cytoskeleton
• Molecular function: Rho guanyl-nucleotide exchange factor activity;cytoskeletal protein binding;Rac guanyl-nucleotide exchange factor activity