FGD3

FYVE, RhoGEF and PH domain containing 3, the group of Dbl family Rho GEFs|Zinc fingers FYVE-type|Pleckstrin homology domain containing

Basic information

Region (hg38): 9:92947523-93036236

Links

ENSG00000127084 ∙ NCBI:89846 ∙ OMIM:617554 ∙ HGNC:16027 ∙ Uniprot:Q5JSP0 ∙ 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 FGD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGD3 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				1	2	3
missense			57	4		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	5	2

Variants in FGD3

This is a list of pathogenic ClinVar variants found in the FGD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-92976263-T-A		not specified	Uncertain significance (Aug 05, 2024)
9-92976273-G-T		not specified	Uncertain significance (Aug 30, 2021)
9-92976303-C-T		not specified	Uncertain significance (Sep 24, 2024)
9-92976333-G-A		not specified	Uncertain significance (Sep 14, 2023)
9-92976491-G-A		not specified	Uncertain significance (Nov 07, 2022)
9-92976530-T-C		not specified	Uncertain significance (Jul 30, 2024)
9-92976584-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-92976636-A-C		not specified	Uncertain significance (Oct 13, 2023)
9-92976674-C-A		not specified	Uncertain significance (Mar 24, 2023)
9-92976696-C-G		not specified	Uncertain significance (Feb 21, 2024)
9-92976702-T-C		not specified	Likely benign (Mar 29, 2022)
9-93002925-C-T		not specified	Uncertain significance (Jan 23, 2024)
9-93004001-G-A		not specified	Uncertain significance (Nov 20, 2024)
9-93004011-C-T		not specified	Uncertain significance (May 31, 2023)
9-93004028-G-C		not specified	Uncertain significance (Jan 04, 2022)
9-93004117-G-T		not specified	Uncertain significance (Aug 19, 2024)
9-93006038-G-A		not specified	Uncertain significance (Dec 14, 2021)
9-93006053-T-G		not specified	Uncertain significance (Jul 12, 2023)
9-93006083-A-G		not specified	Uncertain significance (Dec 19, 2022)
9-93006085-G-C		not specified	Uncertain significance (Dec 27, 2022)
9-93006137-C-T		not specified	Uncertain significance (Feb 22, 2023)
9-93006139-C-G		not specified	Uncertain significance (Dec 22, 2023)
9-93006174-C-A		not specified	Uncertain significance (Sep 14, 2022)
9-93010255-G-T		not specified	Uncertain significance (Apr 04, 2024)
9-93010265-A-G		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGD3	protein_coding	protein_coding	ENST00000375482	16	88786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000133	0.998	124797	0	29	124826	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	345	443	0.779	0.0000273	4715
Missense in Polyphen		113	171.02	0.66073		1884
Synonymous	0.535	186	196	0.951	0.0000133	1451
Loss of Function	2.73	15	31.5	0.476	0.00000142	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000175	0.000175
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.0000557	0.0000556
South Asian	0.000131	0.000131
Other	0.000343	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes the formation of filopodia. May activate CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Plays a role in regulating the actin cytoskeleton and cell shape (By similarity). {ECO:0000250}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.417
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.2

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.409
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.456

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgd3

Gene ontology

• Biological process: cytoskeleton organization;G protein-coupled receptor signaling pathway;regulation of cell shape;actin cytoskeleton organization;regulation of Rho protein signal transduction;positive regulation of apoptotic process;regulation of GTPase activity;filopodium assembly;regulation of small GTPase mediated signal transduction
• Cellular component: ruffle;cytoplasm;Golgi apparatus;cytosol;cytoskeleton;lamellipodium
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;small GTPase binding;metal ion binding