FGGY

FGGY carbohydrate kinase domain containing

Basic information

Region (hg38): 1:59296637-59810647

Links

ENSG00000172456 ∙ NCBI:55277 ∙ OMIM:611370 ∙ HGNC:25610 ∙ Uniprot:Q96C11 ∙ 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 FGGY gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGGY 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in FGGY

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

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

Position	Type	Phenotype	Significance	ClinVar
1-59321589-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-59321617-G-A		not specified	Uncertain significance (Oct 28, 2023)
1-59321662-A-G		not specified	Uncertain significance (Jan 23, 2024)
1-59321712-T-C		not specified	Uncertain significance (Feb 27, 2023)
1-59340039-C-G		not specified	Uncertain significance (Aug 02, 2021)
1-59340041-G-C		not specified	Uncertain significance (Oct 20, 2023)
1-59340048-C-A		not specified	Uncertain significance (Feb 03, 2022)
1-59346247-G-A		not specified	Likely benign (Dec 08, 2023)
1-59346256-A-G		not specified	Uncertain significance (Dec 19, 2022)
1-59346396-G-A		not specified	Uncertain significance (Jan 10, 2022)
1-59346397-A-G		not specified	Uncertain significance (Jun 23, 2023)
1-59378777-C-T		not specified	Uncertain significance (Dec 03, 2021)
1-59378809-T-C		not specified	Uncertain significance (Jul 06, 2022)
1-59378831-C-G		not specified	Uncertain significance (May 18, 2022)
1-59457019-A-T		not specified	Uncertain significance (Oct 06, 2021)
1-59457020-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-59457044-A-G		not specified	Uncertain significance (Jan 23, 2024)
1-59512350-G-A		not specified	Uncertain significance (Apr 06, 2023)
1-59512377-T-C		not specified	Uncertain significance (Jan 29, 2024)
1-59512392-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-59512398-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-59554153-G-A		not specified	Uncertain significance (Jul 20, 2022)
1-59554187-G-A		not specified	Uncertain significance (Jun 10, 2022)
1-59554222-A-T		not specified	Uncertain significance (Feb 16, 2023)
1-59607810-A-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGGY	protein_coding	protein_coding	ENST00000371218	16	471038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.19e-18	0.0174	124906	3	839	125748	0.00335

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.116	331	325	1.02	0.0000173	3738
Missense in Polyphen		136	134.43	1.0117		1510
Synonymous	-0.670	137	127	1.08	0.00000773	1131
Loss of Function	0.574	29	32.5	0.891	0.00000158	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00455	0.00454
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000382	0.000326
Finnish	0.00462	0.00463
European (Non-Finnish)	0.00485	0.00484
Middle Eastern	0.000382	0.000326
South Asian	0.000981	0.000948
Other	0.00376	0.00375

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Amyotrophic lateral sclerosis (ALS) [MIM:105400]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5- 10% of the cases. {ECO:0000269|PubMed:17671248}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.301
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.7

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.216
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fggy

Gene ontology

• Biological process: pentose metabolic process;carbohydrate phosphorylation;neuron cellular homeostasis
• Cellular component: cellular_component;cell
• Molecular function: D-ribulokinase activity