FGD5

FYVE, RhoGEF and PH domain containing 5, the group of Pleckstrin homology domain containing|Dbl family Rho GEFs|Zinc fingers FYVE-type

Basic information

Region (hg38): 3:14810853-14934571

Links

ENSG00000154783 ∙ NCBI:152273 ∙ OMIM:614788 ∙ HGNC:19117 ∙ Uniprot:Q6ZNL6 ∙ 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 FGD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGD5 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	4	8
missense			89	8	4	101
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			8	2	1	11
Total	0	0	97	14	9

Variants in FGD5

This is a list of pathogenic ClinVar variants found in the FGD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-14819079-G-C		not specified	Uncertain significance (Mar 12, 2024)
3-14819081-G-T		not specified	Uncertain significance (Jan 03, 2022)
3-14819085-C-T		not specified	Uncertain significance (Mar 12, 2024)
3-14819120-G-A		not specified	Likely benign (Apr 25, 2023)
3-14819228-A-G		not specified	Likely benign (Dec 30, 2023)
3-14819270-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-14819286-C-T		not specified	Likely benign (Aug 21, 2023)
3-14819298-A-T		not specified	Uncertain significance (May 18, 2022)
3-14819311-C-A		not specified	Uncertain significance (Apr 12, 2023)
3-14819328-A-G		not specified	Uncertain significance (Jun 21, 2023)
3-14819348-G-A		not specified	Uncertain significance (Dec 11, 2023)
3-14819373-A-G		not specified	Uncertain significance (May 24, 2023)
3-14819376-G-A		not specified	Likely benign (Jun 27, 2023)
3-14819448-C-T		not specified	Uncertain significance (Aug 13, 2021)
3-14819499-T-G		not specified	Uncertain significance (Aug 28, 2023)
3-14819522-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-14819549-G-C		not specified	Uncertain significance (May 15, 2023)
3-14819596-G-C		not specified	Uncertain significance (Oct 13, 2021)
3-14819596-G-T		not specified	Uncertain significance (May 01, 2024)
3-14819649-A-G		not specified	Uncertain significance (Jul 13, 2022)
3-14819690-C-T		not specified	Uncertain significance (Feb 05, 2024)
3-14819693-G-A		not specified	Uncertain significance (Mar 14, 2023)
3-14819709-C-T		not specified	Likely benign (May 09, 2022)
3-14819719-T-G		not specified	Uncertain significance (Jan 08, 2024)
3-14819739-G-C		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGD5	protein_coding	protein_coding	ENST00000285046	20	115427

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.20e-7	124643	0	6	124649	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.167	830	844	0.984	0.0000513	9466
Missense in Polyphen		275	304.19	0.90403		3322
Synonymous	-0.361	376	367	1.02	0.0000254	2928
Loss of Function	6.46	4	56.4	0.0710	0.00000257	731

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.0000268	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Mediates VEGF-induced CDC42 activation. May regulate proangiogenic action of VEGF in vascular endothelial cells, including network formation, directional movement and proliferation. May play a role in regulating the actin cytoskeleton and cell shape. {ECO:0000269|PubMed:22328776}.

Intolerance Scores

• loftool: 0.172
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.87

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.352
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgd5
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

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;early endosome;endoplasmic reticulum;Golgi apparatus;cytoskeleton;lamellipodium;ruffle membrane
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;small GTPase binding;metal ion binding