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

ENSG00000180263 ∙ NCBI:55785 ∙ OMIM:613520 ∙ HGNC:21740 ∙ Uniprot:Q6ZV73 ∙ 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 FGD6 gene.

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.

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						0
missense			61	8	2	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	61	8	2

Variants in FGD6

This is a list of pathogenic ClinVar variants found in the FGD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-95081528-T-C		not specified	Likely benign (Oct 01, 2024)
12-95084643-C-T		not specified	Uncertain significance (May 18, 2022)
12-95085854-C-T		not specified	Uncertain significance (Oct 06, 2023)
12-95091809-T-C		not specified	Uncertain significance (Nov 15, 2024)
12-95094621-T-A		not specified	Uncertain significance (Aug 11, 2024)
12-95105045-C-G		not specified	Uncertain significance (Dec 28, 2023)
12-95107576-C-G		not specified	Uncertain significance (Nov 09, 2023)
12-95108416-T-C		not specified	Uncertain significance (Sep 16, 2021)
12-95108534-G-A		not specified	Uncertain significance (Nov 10, 2024)
12-95137538-A-G		not specified	Uncertain significance (Oct 20, 2024)
12-95137542-C-T		not specified	Uncertain significance (Sep 03, 2024)
12-95137593-T-C		not specified	Uncertain significance (Feb 14, 2023)
12-95137642-C-A		not specified	Uncertain significance (Aug 21, 2024)
12-95141380-A-C			Benign (Apr 20, 2018)
12-95141392-G-A		not specified	Uncertain significance (Aug 01, 2024)
12-95141428-G-A		not specified	Uncertain significance (Nov 03, 2022)
12-95141439-T-C		not specified	Uncertain significance (Jan 26, 2022)
12-95141479-G-A		not specified	Uncertain significance (Dec 17, 2023)
12-95152845-T-A			Benign (Apr 20, 2018)
12-95152943-G-C		not specified	Uncertain significance (Aug 27, 2024)
12-95152963-G-A		not specified	Uncertain significance (Dec 08, 2023)
12-95152977-A-C		not specified	Uncertain significance (Jul 20, 2021)
12-95172626-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-95172638-A-T		not specified	Uncertain significance (Jul 10, 2024)
12-95172699-G-T		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

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: 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

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

Mouse Genome Informatics

• Gene name: Fgd6

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