ALG10B

ALG10 alpha-1,2-glucosyltransferase B, the group of Alpha-1,2-glucosyltransferases

Basic information

Region (hg38): 12:38316762-38329721

Links

ENSG00000175548 ∙ NCBI:144245 ∙ OMIM:603313 ∙ HGNC:31088 ∙ Uniprot:Q5I7T1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• long QT syndrome 2 (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ALG10B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALG10B 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	1
missense			40	6		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	6	1

Variants in ALG10B

This is a list of pathogenic ClinVar variants found in the ALG10B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-38316901-A-C		not specified	Uncertain significance (Feb 01, 2025)
12-38316940-C-G		not specified	Uncertain significance (Apr 14, 2022)
12-38316967-C-G		not specified	Uncertain significance (Dec 03, 2024)
12-38316997-A-G		not specified	Uncertain significance (Dec 02, 2024)
12-38316999-A-T		not specified	Uncertain significance (Jan 01, 2025)
12-38317013-C-A		not specified	Uncertain significance (Mar 08, 2025)
12-38317056-C-G		not specified	Uncertain significance (Sep 04, 2024)
12-38318266-T-A		not specified	Uncertain significance (Jul 13, 2022)
12-38318274-T-C		not specified	Uncertain significance (Feb 28, 2024)
12-38318319-A-C		not specified	Uncertain significance (Jul 20, 2022)
12-38318352-A-G		not specified	Uncertain significance (Dec 05, 2024)
12-38318448-C-T		not specified	Uncertain significance (Feb 23, 2025)
12-38320168-C-G			Uncertain significance (-)
12-38320177-A-G		not specified	Uncertain significance (Jul 05, 2023)
12-38320195-T-C		not specified	Uncertain significance (Jan 22, 2024)
12-38320232-C-A		not specified	Uncertain significance (Oct 02, 2023)
12-38320263-T-A		not specified	Uncertain significance (Dec 21, 2023)
12-38320297-A-G		not specified	Uncertain significance (Mar 27, 2023)
12-38320318-C-G		not specified	Uncertain significance (Apr 20, 2024)
12-38320458-A-G		not specified	Uncertain significance (Jun 09, 2022)
12-38320468-C-A		not specified	Uncertain significance (Mar 05, 2025)
12-38320549-T-G			Likely benign (May 01, 2023)
12-38320572-G-A		not specified	Uncertain significance (Mar 01, 2023)
12-38320590-T-C		not specified	Uncertain significance (Oct 01, 2024)
12-38320593-G-A		not specified	Uncertain significance (Nov 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALG10B	protein_coding	protein_coding	ENST00000308742	3	7405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.03e-8	0.257	125447	1	300	125748	0.00120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.57	295	228	1.29	0.0000107	3107
Missense in Polyphen		102	81.974	1.2443		1106
Synonymous	1.05	71	83.2	0.854	0.00000385	911
Loss of Function	0.509	13	15.1	0.859	6.51e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0108	0.0107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000731	0.000730
Middle Eastern	0.000326	0.000326
South Asian	0.000556	0.000555
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative alpha-1,2-glucosyltransferase, which adds the third glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc(2)Man(9)GlcNAc(2)-PP-Dol (By similarity). When coupled to KCNH2 may reduce KCNH2 sensitivity to classic proarrhythmic drug blockade, possibly by mediating glycosylation of KCNH2 (PubMed:14525949). Has a role in maintenance of cochlear outer hair cell function (By similarity). {ECO:0000250|UniProtKB:P50076, ECO:0000250|UniProtKB:Q3UGP8, ECO:0000269|PubMed:14525949}.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Disopyramide Action Pathway;Procainamide (Antiarrhythmic) Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Fosphenytoin (Antiarrhythmic) Action Pathway;Bopindolol Action Pathway;Timolol Action Pathway;Carteolol Action Pathway;Bevantolol Action Pathway;Practolol Action Pathway;Dobutamine Action Pathway;Isoprenaline Action Pathway;Arbutamine Action Pathway;Amiodarone Action Pathway;Levobunolol Action Pathway;Metipranolol Action Pathway;Mexiletine Action Pathway;Lidocaine (Antiarrhythmic) Action Pathway;Quinidine Action Pathway;Sotalol Action Pathway;Epinephrine Action Pathway;Betaxolol Action Pathway;Atenolol Action Pathway;Alprenolol Action Pathway;Acebutolol Action Pathway;Muscle/Heart Contraction;Diltiazem Action Pathway;Propranolol Action Pathway;Pindolol Action Pathway;Penbutolol Action Pathway;Oxprenolol Action Pathway;Metoprolol Action Pathway;Esmolol Action Pathway;Bisoprolol Action Pathway;Bupranolol Action Pathway;Nebivolol Action Pathway;Amlodipine Action Pathway;Verapamil Action Pathway;Nitrendipine Action Pathway;Nisoldipine Action Pathway;Nimodipine Action Pathway;Ibutilide Action Pathway;Tocainide Action Pathway;Flecainide Action Pathway;Isradipine Action Pathway;Nifedipine Action Pathway;Felodipine Action Pathway;Nadolol Action Pathway;Carvedilol Action Pathway;Labetalol Action Pathway;Post-translational protein modification;Metabolism of proteins;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0839

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 1.55
• rvis_percentile_EVS: 95.64

Haploinsufficiency Scores

• pHI: 0.0881
• hipred: N
• hipred_score: 0.358
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Alg10b
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: protein glycosylation;dolichol-linked oligosaccharide biosynthetic process;positive regulation of protein glycosylation;positive regulation of inward rectifier potassium channel activity
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity;transferase activity;dolichyl pyrophosphate Glc2Man9GlcNAc2 alpha-1,2-glucosyltransferase activity