MAN1A2
Basic information
Region (hg38): 1:117367449-117528872
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (40 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAN1A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006699.5. 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 | 1 | |||||
missense | 40 | 40 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 40 | 0 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MAN1A2 | protein_coding | protein_coding | ENST00000356554 | 13 | 161424 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.999 | 0.00108 | 125741 | 0 | 6 | 125747 | 0.0000239 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.56 | 211 | 345 | 0.612 | 0.0000171 | 4185 |
Missense in Polyphen | 26 | 93.945 | 0.27676 | 1164 | ||
Synonymous | 0.104 | 117 | 118 | 0.988 | 0.00000542 | 1233 |
Loss of Function | 4.84 | 3 | 33.0 | 0.0908 | 0.00000176 | 412 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000616 | 0.0000615 |
Ashkenazi Jewish | 0.0000997 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000464 | 0.0000462 |
European (Non-Finnish) | 0.0000264 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the maturation of Asn-linked oligosaccharides. Progressively trim alpha-1,2-linked mannose residues from Man(9)GlcNAc(2) to produce Man(5)GlcNAc(2).;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);N-Glycan biosynthesis - Homo sapiens (human);Vesicle-mediated transport;er associated degradation (erad) pathway;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;N-glycan trimming and elongation in the cis-Golgi;Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2;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
- 0.100
Intolerance Scores
- loftool
- 0.213
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.45
Haploinsufficiency Scores
- pHI
- 0.509
- hipred
- Y
- hipred_score
- 0.688
- ghis
- 0.532
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.528
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Man1a2
- Phenotype
- respiratory system phenotype; 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); 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); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- protein glycosylation;N-glycan processing;respiratory gaseous exchange;lung alveolus development;Golgi apparatus mannose trimming
- Cellular component
- Golgi membrane;endoplasmic reticulum;Golgi apparatus;membrane;integral component of membrane;extracellular exosome
- Molecular function
- mannosyl-oligosaccharide 1,2-alpha-mannosidase activity;calcium ion binding