ALG5

ALG5 dolichyl-phosphate beta-glucosyltransferase, the group of Glycosyltransferase family 2

Basic information

Region (hg38): 13:36949738-37000763

Links

ENSG00000120697NCBI:29880OMIM:604565HGNC:20266Uniprot:Q9Y673AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • polycystic kidney disease 7 (Limited), mode of inheritance: AD
  • polycystic kidney disease 7 (Strong), mode of inheritance: AD
  • polycystic kidney disease 7 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Polycystic kidney disease 7ADRenalTreatment for hypertension and end-stage renal disease is frequently required, and nephrotoxic agents should be avoidedGastrointestinal; Renal35896117

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ALG5 gene.

  • not_specified (36 variants)
  • Polycystic_kidney_disease_7 (14 variants)
  • ALG5-related_disorder (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALG5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013338.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
clinvar
4
missense
3
clinvar
38
clinvar
6
clinvar
47
nonsense
1
clinvar
2
clinvar
1
clinvar
4
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 5 3 39 8 2

Highest pathogenic variant AF is 0.00000373129

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ALG5protein_codingprotein_codingENST00000239891 1050487
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4630.5361257370111257480.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.011431810.7900.00001002087
Missense in Polyphen3159.8270.51816634
Synonymous-0.2796562.21.040.00000321628
Loss of Function3.50523.20.2150.00000145238

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008750.0000875
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004630.0000462
European (Non-Finnish)0.00004810.0000439
Middle Eastern0.000.00
South Asian0.00007430.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Pathway
N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;dolichyl-diphosphooligosaccharide biosynthesis;Synthesis of dolichyl-phosphate-glucose;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

pRec
0.150

Intolerance Scores

loftool
0.551
rvis_EVS
0.08
rvis_percentile_EVS
60.09

Haploinsufficiency Scores

pHI
0.319
hipred
N
hipred_score
0.488
ghis
0.516

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.949

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Alg5
Phenotype
embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
protein glycosylation;protein N-linked glycosylation;determination of left/right symmetry;protein N-linked glycosylation via asparagine
Cellular component
endoplasmic reticulum membrane;membrane;integral component of membrane
Molecular function
oligosaccharyl transferase activity;dolichyl-phosphate beta-glucosyltransferase activity