FGGY

protein-coding

FGGY carbohydrate kinase domain containing

Gene summary

This gene encodes a protein that phosphorylates carbohydrates such as ribulose, ribitol, and L-arabinitol. Genome-wide association studies in some populations have found an association between polymorphisms in this gene and sporadic amyotrophic lateral sclerosis, but studies of other populations have not been able to replicate this association. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

MANE transcript

NM_018291.5

Inheritance

—

ClinVar variants

U:98B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr1:59,296,638-59,810,647

External References & Databases

Ensembl (ENSG00000172456)

Transcript & Mutation Effects

hg38 • Region Span ~514.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FGGY variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018291.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			90 clinvar	2 clinvar		92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	98	2	0	100

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 156 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018291.5	RefSeq	NP_060761.3	15	MANE Select
ENST00000303721.12	Ensembl	ENSP00000305922.8	15	MANE Select
NM_001113411.2	RefSeq	NP_001106882.1	16	Standard
NM_001244714.2	RefSeq	NP_001231643.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

pentose metabolic process
carbohydrate phosphorylation
neuron cellular homeostasis

Molecular Function

D-ribulokinase activity

Cellular Component

cellular_component
cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371218
Coding exons: 16
Length: 471038
Individuals with no LoFs: 124906
Homozygous LoFs: 3
Heterozygous LoFs: 839
Defined: 125748
p: 0.00335

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.116	331	325	1.02	0.0000173	3738
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.0031	0.0031	notable
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00038	0.00033	rare
Finnish	0.0046	0.0046	notable
European (Non-Finnish)	0.0048	0.0048	notable
South Asian	0.00098	0.00095	rare
Other	0.0038	0.0038	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.158

Gene Damage Prediction

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