MAGI1
Basic information
Region (hg38): 3:65353525-66038918
Previous symbols: [ "BAIAP1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (123 variants)
- not_provided (10 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGI1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001033057.2. 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 | 4 | |||||
missense | 122 | 128 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 122 | 9 | 2 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MAGI1 | protein_coding | protein_coding | ENST00000402939 | 23 | 685310 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.560 | 0.440 | 125715 | 0 | 33 | 125748 | 0.000131 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.36 | 785 | 900 | 0.872 | 0.0000550 | 9535 |
Missense in Polyphen | 293 | 383.19 | 0.76464 | 4240 | ||
Synonymous | -0.317 | 373 | 365 | 1.02 | 0.0000243 | 2937 |
Loss of Function | 6.17 | 16 | 72.7 | 0.220 | 0.00000443 | 752 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000268 | 0.000268 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000164 | 0.000163 |
Finnish | 0.0000978 | 0.0000924 |
European (Non-Finnish) | 0.000134 | 0.000132 |
Middle Eastern | 0.000164 | 0.000163 |
South Asian | 0.000170 | 0.000163 |
Other | 0.000170 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role as scaffolding protein at cell-cell junctions. May regulate acid-induced ASIC3 currents by modulating its expression at the cell surface (By similarity). {ECO:0000250}.;
- Pathway
- Tight junction - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Pathways Affected in Adenoid Cystic Carcinoma;EGFR1
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- 0.519
- rvis_EVS
- -1.38
- rvis_percentile_EVS
- 4.36
Haploinsufficiency Scores
- pHI
- 0.272
- hipred
- Y
- hipred_score
- 0.793
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.824
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Magi1
- Phenotype
Gene ontology
- Biological process
- cell adhesion;signal transduction;cell surface receptor signaling pathway;protein-containing complex assembly
- Cellular component
- nucleoplasm;cytoplasm;plasma membrane;cell-cell junction;adherens junction;bicellular tight junction;cell junction;cell projection
- Molecular function
- protein binding;ATP binding;protein C-terminus binding;protein-containing complex scaffold activity;alpha-actinin binding