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.

not_specified (188 variants)
not_provided (29 variants)

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. These statistics are base on transcript: NM_000014808.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				11 clinvar	2 clinvar	13
missense			175 clinvar	19 clinvar	4 clinvar	198
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	175	30	6

Loading clinvar variants...

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