MAN2A1
mannosidase alpha class 2A member 1, the group of Mannosidases alpha class 2
Basic information
Region (hg38): 5:109689927-109869625
Previous symbols: [ "MANA2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 59 | 64 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 59 | 5 | 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) | ||
| 5-109690447-C-A | not specified | Uncertain significance (May 28, 2024) | ||
| 5-109690500-G-A | not specified | Uncertain significance (Apr 20, 2024) | ||
| 5-109690536-A-G | not specified | Uncertain significance (Sep 25, 2023) | ||
| 5-109690542-C-G | not specified | Uncertain significance (Jul 31, 2024) | ||
| 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) | ||
| 5-109716135-A-G | not specified | Uncertain significance (Nov 24, 2024) | ||
| 5-109716193-C-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 5-109716210-T-C | not specified | Uncertain significance (Apr 20, 2024) | ||
| 5-109716243-C-A | not specified | Uncertain significance (Jan 10, 2022) | ||
| 5-109716256-A-G | not specified | Uncertain significance (Aug 04, 2024) | ||
| 5-109729345-G-T | not specified | Uncertain significance (Jun 26, 2024) | ||
| 5-109729401-A-G | not specified | Uncertain significance (Jun 21, 2021) | ||
| 5-109729429-G-A | not specified | Uncertain significance (Oct 28, 2024) | ||
| 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) | ||
| 5-109755448-A-G | not specified | Uncertain significance (Oct 21, 2024) | ||
| 5-109755455-A-G | not specified | Uncertain significance (Aug 11, 2024) |
GnomAD
Source:
| 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:
- 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