PGGHG
protein-codingprotein-glucosylgalactosylhydroxylysine glucosidase, the group of Glycoside hydrolases
Gene summary
Enables protein-glucosylgalactosylhydroxylysine glucosidase activity. Involved in carbohydrate metabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]
- ATHL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.0 kbGenCC 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 PGGHG variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_025092.5. 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 | 2 | ||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 15 | 2 | 0 | 17 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079368.3 | 13 | MANE Select | |
| Ensembl | ENSP00000387185.2 | 13 | MANE Select | |
| Ensembl | ENSP00000380780.3 | 5 | Standard | |
| Ensembl | ENSP00000387099.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- carbohydrate metabolic process
- trehalose catabolic process
Molecular Function
- alpha,alpha-trehalase activity
- protein-glucosylgalactosylhydroxylysine glucosidase activity
Cellular Component
- cell wall
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000409548
- Coding exons
- 13
- Length
- 6973
- Individuals with no LoFs
- 125573
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 162
- Defined
- 125735
- p
- 0.000644
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.175 | 455 | 466 | 0.977 | 0.0000300 | 4708 |
| Missense (PolyPhen) | 134 | 163.9 | 0.81756 | 1731 | ||
| Synonymous | -1.45 | 237 | 210 | 1.13 | 0.0000151 | 1565 |
| Loss of Function | 1.39 | 26 | 34.8 | 0.747 | 0.00000190 | 330 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0.00014 | 0.000099 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.000096 | 0.000092 | rare |
| European (Non-Finnish) | 0.00088 | 0.00085 | rare |
| South Asian | 0.0014 | 0.0014 | notable |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the hydrolysis of glucose from the disaccharide unit linked to hydroxylysine residues of collagen and collagen-like proteins. {ECO:0000269|PubMed:26682924}.;
Recessive Scores
- pRec
- 0.0964
Intolerance Scores
- RVIS EVS
- -0.7
- RVIS percentile EVS
- 14.81
Essentials
- Essential (gene trap)
- N