FARP1

FERM, ARH/RhoGEF and pleckstrin domain protein 1, the group of Dbl family Rho GEFs|FERM domain containing|Pleckstrin homology domain containing|MicroRNA protein coding host genes|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 13:98142561-98455176

Links

ENSG00000152767 ∙ NCBI:10160 ∙ OMIM:602654 ∙ HGNC:3591 ∙ Uniprot:Q9Y4F1 ∙ 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 FARP1 gene.

• Inborn genetic diseases (62 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FARP1 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				2	2	4
missense			44			44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			18			18
Total	0	0	62	2	2

Variants in FARP1

This is a list of pathogenic ClinVar variants found in the FARP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-98176170-T-G		not specified	Uncertain significance (Feb 09, 2022)
13-98176350-G-A		not specified	Uncertain significance (Dec 07, 2021)
13-98176351-G-A		not specified	Likely benign (Feb 12, 2024)
13-98176374-G-A		not specified	Uncertain significance (Feb 07, 2023)
13-98176495-C-T		not specified	Uncertain significance (Jul 14, 2021)
13-98176591-C-T		not specified	Uncertain significance (Oct 12, 2021)
13-98176674-C-T		not specified	Uncertain significance (Nov 10, 2022)
13-98176701-G-C		not specified	Uncertain significance (Dec 09, 2023)
13-98176731-G-A		not specified	Uncertain significance (Aug 04, 2023)
13-98176781-G-C		not specified	Uncertain significance (Sep 06, 2022)
13-98176876-C-T		not specified	Uncertain significance (Dec 15, 2021)
13-98176882-C-T		not specified	Uncertain significance (Nov 07, 2023)
13-98176944-C-T		not specified	Uncertain significance (Apr 28, 2023)
13-98176945-G-A		not specified	Uncertain significance (Dec 13, 2022)
13-98176966-C-T		not specified	Uncertain significance (Oct 14, 2023)
13-98176986-T-G		not specified	Uncertain significance (Dec 09, 2023)
13-98177006-G-T		not specified	Uncertain significance (Feb 15, 2023)
13-98177061-G-C		not specified	Uncertain significance (Feb 17, 2024)
13-98177104-C-T		not specified	Uncertain significance (Jan 23, 2023)
13-98177130-C-T		not specified	Uncertain significance (Apr 27, 2022)
13-98177134-T-C		not specified	Uncertain significance (Apr 28, 2023)
13-98177157-C-A		not specified	Uncertain significance (May 27, 2022)
13-98177158-G-A		not specified	Uncertain significance (Jun 12, 2023)
13-98177197-C-T		not specified	Uncertain significance (Mar 03, 2022)
13-98177233-C-G		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FARP1	protein_coding	protein_coding	ENST00000319562	26	307212

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000507	1.00	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.836	593	653	0.908	0.0000424	6885
Missense in Polyphen		196	243.69	0.80429		2603
Synonymous	-0.774	298	281	1.06	0.0000208	1983
Loss of Function	4.55	20	57.1	0.350	0.00000277	654

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000729	0.000721
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as guanine nucleotide exchange factor for RAC1. May play a role in semaphorin signaling. Plays a role in the assembly and disassembly of dendritic filopodia, the formation of dendritic spines, regulation of dendrite length and ultimately the formation of synapses (By similarity). {ECO:0000250}.
• Pathway: Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.468
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.97

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.492
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.220

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Farp1

Zebrafish Information Network

• Gene name: farp1
• Affected structure: YSL
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: synapse assembly;negative regulation of phosphatase activity;regulation of Rho protein signal transduction;dendrite morphogenesis
• Cellular component: cytosol;cytoskeleton;cell junction;filopodium;dendrite;extrinsic component of cytoplasmic side of plasma membrane;dendritic spine
• Molecular function: Rho guanyl-nucleotide exchange factor activity;cytoskeletal protein binding;Rac guanyl-nucleotide exchange factor activity