GPM6A
Basic information
Region (hg38): 4:175632934-176002664
Previous symbols: [ "GPM6" ]
Links
Phenotypes
GenCC
Source:
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 GPM6A 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in GPM6A
This is a list of pathogenic ClinVar variants found in the GPM6A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-175635000-T-C | not specified | Uncertain significance (Aug 20, 2024) | ||
| 4-175635003-G-C | not specified | Uncertain significance (Aug 22, 2023) | ||
| 4-175812196-T-G | not specified | Uncertain significance (Aug 21, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GPM6A | protein_coding | protein_coding | ENST00000280187 | 7 | 369731 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.990 | 0.0104 | 124505 | 0 | 1 | 124506 | 0.00000402 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.96 | 89 | 159 | 0.561 | 0.00000841 | 1822 |
| Missense in Polyphen | 27 | 75.109 | 0.35948 | 876 | ||
| Synonymous | 0.00284 | 59 | 59.0 | 1.00 | 0.00000341 | 531 |
| Loss of Function | 3.43 | 0 | 13.7 | 0.00 | 5.81e-7 | 173 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000891 | 0.00000891 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in neuronal differentiation, including differentiation and migration of neuronal stem cells. Plays a role in neuronal plasticity and is involved in neurite and filopodia outgrowth, filopodia motility and probably synapse formation. GPM6A-induced filopodia formation involves mitogen-activated protein kinase (MAPK) and Src signaling pathways. May be involved in neuronal NGF-dependent Ca(2+) influx. May be involved in regulation of endocytosis and intracellular trafficking of G- protein-coupled receptors (GPCRs); enhances internalization and recycling of mu-type opioid receptor. {ECO:0000269|PubMed:19298174}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.0445
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.806
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.655
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.185
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gpm6a
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype;
Gene ontology
- Biological process
- neuron migration;neural retina development;synapse assembly;response to bacterium;neuron projection development;neuron projection morphogenesis;stem cell differentiation;regulation of synapse organization;positive regulation of filopodium assembly;calcium ion transmembrane transport
- Cellular component
- plasma membrane;filopodium;neuron projection;neuronal cell body;dendritic spine;axonal growth cone;extracellular exosome;glutamatergic synapse;integral component of presynaptic active zone membrane;extracellular vesicle
- Molecular function
- calcium channel activity;protein binding