ALG5

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

Basic information

Region (hg38): 13:36949737-37000763

Links

ENSG00000120697 ∙ NCBI:29880 ∙ OMIM:604565 ∙ HGNC:20266 ∙ Uniprot:Q9Y673 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Polycystic kidney disease 7	AD	Renal	Treatment for hypertension and end-stage renal disease is frequently required, and nephrotoxic agents should be avoided	Gastrointestinal; Renal	35896117

ClinVar

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

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.

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				1	2	3
missense			14	4		18
nonsense		2				2
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					6	6
Total	0	2	15	5	8

Variants in ALG5

This is a list of pathogenic ClinVar variants found in the ALG5 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-36949955-C-T		not specified	Uncertain significance (Sep 22, 2023)
13-36949991-C-A		not specified	Uncertain significance (Oct 30, 2023)
13-36949991-C-T		not specified	Uncertain significance (Oct 12, 2021)
13-36950001-T-C		not specified	Uncertain significance (Jun 28, 2022)
13-36950023-T-G		not specified	Uncertain significance (Dec 15, 2022)
13-36952574-T-C		not specified	Uncertain significance (Jul 06, 2021)
13-36952580-G-C		not specified	Uncertain significance (Jan 08, 2024)
13-36965575-C-T		Polycystic kidney disease 7	Pathogenic (Oct 04, 2022)
13-36965578-C-T		not specified	Uncertain significance (Jul 26, 2022)
13-36965593-G-C		not specified	Uncertain significance (Nov 14, 2023)
13-36965601-C-T		ALG5-related disorder	Likely benign (Oct 04, 2023)
13-36965602-G-A		Polycystic kidney disease 7	Uncertain significance (Mar 25, 2024)
13-36965625-AAAT-A		Polycystic kidney disease 7	Uncertain significance (Nov 29, 2023)
13-36965643-C-G		Polycystic kidney disease 7	Uncertain significance (Apr 04, 2024)
13-36965643-CTG-C		Polycystic kidney disease 7	Pathogenic (Oct 04, 2022)
13-36965654-T-C		not specified	Uncertain significance (Aug 14, 2023)
13-36965676-C-T		Polycystic kidney disease 7	Likely pathogenic (Dec 06, 2023)
13-36965713-C-T		Polycystic kidney disease 7	Pathogenic (Oct 04, 2022)
13-36965714-G-A		ALG5-related disorder	Uncertain significance (May 09, 2023)
13-36965725-C-T		Polycystic kidney disease 7	Pathogenic (Oct 04, 2022)
13-36971985-T-C		ALG5-related disorder	Uncertain significance (Dec 26, 2023)
13-36985628-G-C		not specified	Uncertain significance (Dec 20, 2021)
13-36993668-C-T		not specified	Likely benign (Dec 15, 2022)
13-36995037-T-C		Polycystic kidney disease 7	Likely pathogenic (May 02, 2024)
13-36995455-C-T		ALG5-related disorder • not specified	Conflicting classifications of pathogenicity (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALG5	protein_coding	protein_coding	ENST00000239891	10	50487

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.463	0.536	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	143	181	0.790	0.0000100	2087
Missense in Polyphen		31	59.827	0.51816		634
Synonymous	-0.279	65	62.2	1.04	0.00000321	628
Loss of Function	3.50	5	23.2	0.215	0.00000145	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000875	0.0000875
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000481	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000743	0.0000653
Other	0.00	0.00

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

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

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