MAGED2
Basic information
Region (hg38): X:54807599-54816015
Links
Phenotypes
GenCC
Source:
- Bartter disease type 5 (Strong), mode of inheritance: XL
- antenatal Bartter syndrome (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Bartter syndrome type 5, antenatal transient | XL | Renal | The condition can involve prenatal and postnatal manifestations, and awareness may allow medical management of electrolyte abnormalities during the transient period when children are affected | Renal | 27120771 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (93 variants)
- Inborn_genetic_diseases (38 variants)
- Bartter_disease_type_5 (17 variants)
- MAGED2-related_disorder (7 variants)
- Hypoplasia_of_the_corpus_callosum (1 variants)
- Hypotonia (1 variants)
- Global_developmental_delay (1 variants)
- Attention_deficit_hyperactivity_disorder (1 variants)
- Dandy-Walker_syndrome (1 variants)
- Cerebellar_atrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGED2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000177433.3. 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 | 17 | 30 | ||||
missense | 55 | 69 | ||||
nonsense | 8 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
Total | 9 | 5 | 63 | 26 | 13 |
Highest pathogenic variant AF is 9.73339e-7
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MAGED2 | protein_coding | protein_coding | ENST00000375068 | 11 | 8414 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.995 | 0.00462 | 125280 | 0 | 1 | 125281 | 0.00000399 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.34 | 128 | 227 | 0.563 | 0.0000179 | 3892 |
Missense in Polyphen | 33 | 71.623 | 0.46074 | 1336 | ||
Synonymous | 0.538 | 77 | 83.2 | 0.925 | 0.00000643 | 1223 |
Loss of Function | 3.97 | 1 | 20.3 | 0.0492 | 0.00000168 | 343 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000633 | 0.0000471 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates the expression, localization to the plasma membrane and function of the sodium chloride cotransporters SLC12A1 and SLC12A3, two key components of salt reabsorption in the distal renal tubule. {ECO:0000269|PubMed:27120771}.;
- Pathway
- Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- loftool
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 37.32
Haploinsufficiency Scores
- pHI
- 0.513
- hipred
- N
- hipred_score
- 0.496
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.788
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Maged2
- Phenotype
Gene ontology
- Biological process
- platelet degranulation;female pregnancy;renal sodium ion absorption
- Cellular component
- extracellular region;nucleus;nucleolus;cytosol;membrane;platelet alpha granule lumen
- Molecular function
- protein binding