FGD6
Basic information
Region (hg38): 12:95076749-95217482
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (162 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGD6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018351.4. 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 | 0 | |||||
missense | 147 | 15 | 163 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 147 | 15 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FGD6 | protein_coding | protein_coding | ENST00000343958 | 21 | 140734 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.40e-8 | 1.00 | 125720 | 0 | 28 | 125748 | 0.000111 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.966 | 667 | 741 | 0.900 | 0.0000368 | 9486 |
Missense in Polyphen | 122 | 170.44 | 0.7158 | 2244 | ||
Synonymous | 1.21 | 240 | 265 | 0.905 | 0.0000134 | 2597 |
Loss of Function | 4.59 | 25 | 64.9 | 0.385 | 0.00000318 | 884 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000207 | 0.000207 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000273 | 0.000272 |
Finnish | 0.0000464 | 0.0000462 |
European (Non-Finnish) | 0.0000889 | 0.0000879 |
Middle Eastern | 0.000273 | 0.000272 |
South Asian | 0.000165 | 0.000163 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May activate CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. May play a role in regulating the actin cytoskeleton and cell shape (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0913
Intolerance Scores
- loftool
- 0.519
- rvis_EVS
- -1.08
- rvis_percentile_EVS
- 7.32
Haploinsufficiency Scores
- pHI
- 0.184
- hipred
- N
- hipred_score
- 0.399
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.138
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fgd6
- Phenotype
Gene ontology
- Biological process
- cytoskeleton organization;regulation of cell shape;actin cytoskeleton organization;regulation of Rho protein signal transduction;regulation of GTPase activity;filopodium assembly
- Cellular component
- ruffle;cytoplasm;Golgi apparatus;cytoskeleton;lamellipodium
- Molecular function
- guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;small GTPase binding;metal ion binding