MAN2A1
Basic information
Region (hg38): 5:109689927-109869625
Previous symbols: [ "MANA2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (144 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. These statistics are base on transcript: NM_000002372.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 135 | 144 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 135 | 9 | 0 |
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