FARP1
Basic information
Region (hg38): 13:98142562-98455176
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 4 | |||||
missense | 57 | 57 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 25 | 26 | ||||
Total | 0 | 0 | 82 | 3 | 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) | ||
13-98176660-G-A | not specified | Uncertain significance (Jun 17, 2024) | ||
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) | ||
13-98176926-C-T | not specified | Uncertain significance (May 13, 2024) | ||
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) |
GnomAD
Source:
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:
- 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
- Phenotype
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