FGD2

FYVE, RhoGEF and PH domain containing 2, the group of Pleckstrin homology domain containing|Zinc fingers FYVE-type|Dbl family Rho GEFs

Basic information

Region (hg38): 6:37005646-37029299

Links

ENSG00000146192 ∙ NCBI:221472 ∙ OMIM:605091 ∙ HGNC:3664 ∙ Uniprot:Q7Z6J4 ∙ 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 FGD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGD2 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	4	5
missense			63	2	4	69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	63	3	8

Variants in FGD2

This is a list of pathogenic ClinVar variants found in the FGD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-37005824-G-A		not specified	Uncertain significance (Nov 07, 2024)
6-37005860-C-G		not specified	Uncertain significance (Dec 28, 2024)
6-37008873-C-A			Benign (Feb 25, 2018)
6-37008873-C-G		not specified	Uncertain significance (May 17, 2023)
6-37008878-A-C		not specified	Uncertain significance (Jul 30, 2024)
6-37008878-A-G			Benign (Aug 02, 2017)
6-37008884-G-A		not specified	Likely benign (Jan 01, 2025)
6-37008884-G-T		not specified	Uncertain significance (Apr 14, 2022)
6-37008920-G-A		not specified	Uncertain significance (Jul 26, 2024)
6-37008946-G-A			Benign (Apr 16, 2018)
6-37008987-C-A		not specified	Uncertain significance (Jan 04, 2022)
6-37008989-C-G		not specified	Uncertain significance (May 20, 2024)
6-37009009-A-G		not specified	Uncertain significance (Apr 20, 2023)
6-37009061-C-T		not specified	Likely benign (Sep 16, 2021)
6-37010984-G-T		not specified	Uncertain significance (Jan 06, 2023)
6-37010990-C-G		not specified	Uncertain significance (Dec 14, 2023)
6-37010991-G-A		not specified	Uncertain significance (Aug 04, 2024)
6-37010992-T-C		not specified	Uncertain significance (Jul 30, 2024)
6-37011017-G-T		not specified	Uncertain significance (Nov 23, 2021)
6-37011030-C-T		not specified	Uncertain significance (Mar 14, 2023)
6-37011734-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-37011737-G-A		not specified	Uncertain significance (Oct 12, 2024)
6-37011742-A-G		not specified	Uncertain significance (Jun 07, 2023)
6-37011766-G-A		not specified	Uncertain significance (Sep 22, 2023)
6-37011773-T-C		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGD2	protein_coding	protein_coding	ENST00000274963	16	23425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.71e-9	0.992	125641	0	106	125747	0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.705	371	411	0.902	0.0000262	4240
Missense in Polyphen		140	164.83	0.84934		1635
Synonymous	-0.756	181	169	1.07	0.0000107	1293
Loss of Function	2.46	19	34.6	0.549	0.00000165	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000539	0.000539
Ashkenazi Jewish	0.00	0.00
East Asian	0.00370	0.00370
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.00370	0.00370
South Asian	0.0000709	0.0000653
Other	0.000328	0.000326

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. Activates JNK1 via CDC42 but not RAC1. Binds to phosphatidylinositol 4,5-bisphosphate, phosphatidylinositol 3,4,5- trisphosphate, phosphatidylinositol 5-monophosphate, phosphatidylinositol 4-monophosphate and phosphatidylinositol 3- monophosphate (By similarity). {ECO:0000250}.
• Pathway: 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: 0.103

Intolerance Scores

• loftool: 0.464
• rvis_EVS: 0.45
• rvis_percentile_EVS: 78.02

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.414
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgd2
• Phenotype: reproductive system phenotype

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;positive regulation of JUN kinase activity;filopodium assembly;regulation of small GTPase mediated signal transduction
• Cellular component: ruffle;nucleus;cytoplasm;Golgi apparatus;cytosol;cytoskeleton;lamellipodium;early endosome membrane;ruffle membrane
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;small GTPase binding;metal ion binding;phosphatidylinositol phosphate binding