MAN2A1

mannosidase alpha class 2A member 1, the group of Mannosidases alpha class 2

Basic information

Region (hg38): 5:109689926-109869625

Previous symbols: [ "MANA2" ]

Links

ENSG00000112893 ∙ NCBI:4124 ∙ OMIM:154582 ∙ HGNC:6824 ∙ Uniprot:Q16706 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAN2A1 gene.

• Inborn genetic diseases (48 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAN2A1 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						0
missense			45	3		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	45	3	1

Variants in MAN2A1

This is a list of pathogenic ClinVar variants found in the MAN2A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-109690445-T-G		not specified	Uncertain significance (Dec 22, 2023)
5-109690536-A-G		not specified	Uncertain significance (Sep 25, 2023)
5-109713524-A-C		not specified	Uncertain significance (Nov 02, 2023)
5-109713532-A-G		not specified	Uncertain significance (Dec 11, 2023)
5-109713568-C-G		not specified	Uncertain significance (May 25, 2022)
5-109713578-A-G		not specified	Uncertain significance (Sep 18, 2023)
5-109713674-G-A		not specified	Uncertain significance (Aug 05, 2023)
5-109713730-T-C		not specified	Uncertain significance (Oct 10, 2023)
5-109716127-A-G		not specified	Uncertain significance (Dec 02, 2022)
5-109716243-C-A		not specified	Uncertain significance (Jan 10, 2022)
5-109729401-A-G		not specified	Uncertain significance (Jun 21, 2021)
5-109729479-A-G		not specified	Uncertain significance (Dec 13, 2022)
5-109729489-T-C		not specified	Uncertain significance (Aug 02, 2022)
5-109755416-T-A		not specified	Uncertain significance (Jun 05, 2023)
5-109767553-G-C		not specified	Uncertain significance (Mar 29, 2022)
5-109767639-G-A		not specified	Uncertain significance (Jun 22, 2023)
5-109767648-G-A		not specified	Uncertain significance (Sep 15, 2021)
5-109770384-C-T		not specified	Uncertain significance (Mar 31, 2023)
5-109770505-C-G		not specified	Uncertain significance (Oct 05, 2021)
5-109770516-A-G		not specified	Uncertain significance (Mar 02, 2023)
5-109774793-G-A		not specified	Likely benign (Dec 13, 2023)
5-109774814-G-T		not specified	Uncertain significance (Oct 13, 2023)
5-109774877-A-T		not specified	Uncertain significance (Dec 07, 2021)
5-109774901-T-C		not specified	Uncertain significance (Aug 31, 2022)
5-109774948-T-A		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAN2A1	protein_coding	protein_coding	ENST00000261483	22	180260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-10	1.00	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.427	560	589	0.950	0.0000296	7510
Missense in Polyphen		142	240.84	0.5896		3144
Synonymous	-2.80	263	211	1.25	0.0000108	2115
Loss of Function	3.98	27	60.3	0.448	0.00000309	754

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000303
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.00	0.00
Finnish	0.0000532	0.0000462
European (Non-Finnish)	0.0000902	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000209	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway. {ECO:0000250|UniProtKB:P28494}.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Reactions specific to the complex N-glycan synthesis pathway;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;N-Glycan biosynthesis;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.294

Intolerance Scores

• loftool: 0.243
• rvis_EVS: -1.57
• rvis_percentile_EVS: 3.2

Haploinsufficiency Scores

• pHI: 0.498
• hipred: Y
• hipred_score: 0.544
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.352

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Man2a1
• Phenotype: renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; hematopoietic system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands 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); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: in utero embryonic development;liver development;mannose metabolic process;protein glycosylation;N-glycan processing;protein deglycosylation;mitochondrion organization;vacuole organization;respiratory gaseous exchange;lung alveolus development;positive regulation of neurogenesis;retina morphogenesis in camera-type eye
• Cellular component: Golgi membrane;Golgi medial cisterna;cis-Golgi network;membrane;integral component of membrane;extracellular exosome
• Molecular function: alpha-mannosidase activity;mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity;hydrolase activity, hydrolyzing N-glycosyl compounds;carbohydrate binding;metal ion binding