FGD6

FYVE, RhoGEF and PH domain containing 6, the group of Dbl family Rho GEFs|Pleckstrin homology domain containing|Zinc fingers FYVE-type

Basic information

Region (hg38): 12:95076749-95217482

Links

ENSG00000180263NCBI:55785OMIM:613520HGNC:21740Uniprot:Q6ZV73AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FGD6 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
147
clinvar
15
clinvar
1
clinvar
163
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 147 15 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FGD6protein_codingprotein_codingENST00000343958 21140734
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.40e-81.001257200281257480.000111
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9666677410.9000.00003689486
Missense in Polyphen122170.440.71582244
Synonymous1.212402650.9050.00001342597
Loss of Function4.592564.90.3850.00000318884

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002070.000207
Ashkenazi Jewish0.000.00
East Asian0.0002730.000272
Finnish0.00004640.0000462
European (Non-Finnish)0.00008890.0000879
Middle Eastern0.0002730.000272
South Asian0.0001650.000163
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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