FARP1

protein-coding

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

Gene summary

This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

MANE transcript

NM_005766.4

Inheritance

—

ClinVar variants

U:182B:10

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr13:98,142,562-98,455,176

External References & Databases

Ensembl (ENSG00000152767)

Transcript & Mutation Effects

hg38 • Region Span ~312.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FARP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 223

not providedTotal: 4

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005766.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	3 clinvar	2 clinvar	7
missense			173 clinvar	5 clinvar		178
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	182	8	2	192

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005766.4	RefSeq	NP_005757.1	26	MANE Select
ENST00000319562.11	Ensembl	ENSP00000322926.6	26	MANE Select
NM_001001715.4	RefSeq	NP_001001715.2	2	Standard
NM_001286839.2	RefSeq	NP_001273768.1	27	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
farp1	Danio rerio	Structure: YSL Quality: edematous abnormal

Gene / Model

Organism

Observed Phenotype

farp1

Danio rerio

Structure: YSL

Quality: edematous

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Regulation of RhoA activity

Biological Process

synapse assembly
negative regulation of phosphatase activity
regulation of Rho protein signal transduction
dendrite morphogenesis

Molecular Function

Rho guanyl-nucleotide exchange factor activity
cytoskeletal protein binding
Rac guanyl-nucleotide exchange factor activity

Cellular Component

cytosol
cytoskeleton
cell junction
filopodium
dendrite

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319562
Coding exons: 26
Length: 307212
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125748
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.836	593	653	0.908	0.0000424	6885
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00016	0.00016	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.468
RVIS EVS: 0.1
RVIS percentile EVS: 60.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.220

Gene Damage Prediction

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