MAN2B2

mannosidase alpha class 2B member 2, the group of Mannosidases alpha class 2

Basic information

Region (hg38): 4:6575188-6623362

Links

ENSG00000013288 ∙ NCBI:23324 ∙ OMIM:618899 ∙ HGNC:29623 ∙ Uniprot:Q9Y2E5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• MAN2B2 deficiency (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAN2B2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAN2B2 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				5	3	8
missense			99	6	5	110
nonsense		1				1
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					12	12
Total	0	1	100	12	20

Variants in MAN2B2

This is a list of pathogenic ClinVar variants found in the MAN2B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-6575232-C-T		not specified	Uncertain significance (Sep 17, 2021)
4-6575247-C-T		not specified	Uncertain significance (May 16, 2023)
4-6575256-C-A		not specified	Uncertain significance (Nov 13, 2023)
4-6575293-G-A		not specified	Likely benign (Dec 16, 2022)
4-6575316-C-T		not specified	Uncertain significance (Dec 03, 2021)
4-6575322-G-A		MAN2B2-related disorder	Conflicting classifications of pathogenicity (Mar 25, 2024)
4-6575326-T-G		not specified	Uncertain significance (Jan 23, 2024)
4-6575334-G-A		not specified	Uncertain significance (Mar 06, 2023)
4-6575344-T-C		not specified	Uncertain significance (Apr 14, 2022)
4-6575349-G-A		not specified	Uncertain significance (Mar 16, 2021)
4-6576588-G-A		not specified	Likely benign (Nov 08, 2022)
4-6576596-G-A		not specified	Uncertain significance (Jan 09, 2024)
4-6576599-G-A		not specified	Uncertain significance (Sep 16, 2021)
4-6576698-G-A		not specified	Uncertain significance (May 07, 2024)
4-6576716-A-C		not specified	Uncertain significance (Dec 16, 2022)
4-6576719-T-C		not specified	Likely benign (May 13, 2024)
4-6576760-A-G		not specified	Benign (Jan 24, 2024)
4-6578426-T-C		not specified	Uncertain significance (Jul 20, 2022)
4-6578432-A-G		not specified	Uncertain significance (May 11, 2022)
4-6578556-A-G		not specified	Benign (Jan 24, 2024)
4-6587004-G-A		not specified	Uncertain significance (Jun 11, 2021)
4-6587041-TCTC-T		Congenital disorder of glycosylation	Uncertain significance (-)
4-6587095-C-A		not specified	Uncertain significance (Aug 17, 2022)
4-6587110-A-G		not specified	Uncertain significance (Feb 27, 2024)
4-6587125-C-T		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAN2B2	protein_coding	protein_coding	ENST00000285599	19	48188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.56e-23	0.0767	125348	1	399	125748	0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.257	688	669	1.03	0.0000458	6483
Missense in Polyphen		248	234.52	1.0575		2489
Synonymous	0.442	290	300	0.968	0.0000222	2111
Loss of Function	1.49	41	52.6	0.779	0.00000259	518

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00236	0.00228
Ashkenazi Jewish	0.00	0.00
East Asian	0.00925	0.00918
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000679	0.000668
Middle Eastern	0.00925	0.00918
South Asian	0.00288	0.00285
Other	0.00197	0.00196

dbNSFP

Source: dbNSFP

• Pathway: Other glycan degradation - Homo sapiens (human);Lysosomal oligosaccharide catabolism;Metabolism of carbohydrates;Metabolism (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.322
• rvis_EVS: 2.38
• rvis_percentile_EVS: 98.47

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.204
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.463

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Man2b2
• Phenotype: endocrine/exocrine gland 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); immune system phenotype

Gene ontology

• Biological process: mannose metabolic process;protein deglycosylation;oligosaccharide catabolic process
• Cellular component: vacuolar membrane;lysosomal lumen;extracellular exosome
• Molecular function: alpha-mannosidase activity;mannan endo-1,6-alpha-mannosidase activity;carbohydrate binding;metal ion binding