GPM6B
Basic information
Region (hg38): X:13770939-13938638
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 GPM6B 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 | 2 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 2 | 1 |
Variants in GPM6B
This is a list of pathogenic ClinVar variants found in the GPM6B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-13776244-A-G | Benign (May 08, 2018) | |||
| X-13776249-C-T | not specified | Uncertain significance (Mar 14, 2024) | ||
| X-13776267-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| X-13777346-G-A | not specified | Likely benign (Dec 13, 2017) | ||
| X-13777400-G-A | Likely benign (Aug 01, 2022) | |||
| X-13779840-G-C | not specified | Uncertain significance (May 31, 2023) | ||
| X-13779874-G-A | not specified | Uncertain significance (May 23, 2023) | ||
| X-13783381-C-T | not specified | Uncertain significance (Dec 18, 2023) | ||
| X-13783432-G-A | not specified | Uncertain significance (Apr 25, 2023) | ||
| X-13785650-C-T | not specified | Likely benign (Nov 12, 2021) | ||
| X-13816882-G-T | not specified | Uncertain significance (May 06, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GPM6B | protein_coding | protein_coding | ENST00000316715 | 8 | 167608 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.346 | 0.651 | 125475 | 4 | 1 | 125480 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.99 | 68 | 132 | 0.514 | 0.0000104 | 2155 |
| Missense in Polyphen | 13 | 29.236 | 0.44465 | 519 | ||
| Synonymous | -0.413 | 59 | 55.1 | 1.07 | 0.00000508 | 621 |
| Loss of Function | 2.58 | 3 | 13.1 | 0.229 | 9.62e-7 | 211 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000725 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000377 | 0.0000264 |
| Middle Eastern | 0.0000725 | 0.0000544 |
| South Asian | 0.0000714 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in neural development. Involved in regulation of osteoblast function and bone formation. Involved in matrix vesicle release by osteoblasts; this function seems to involve maintenance of the actin cytoskeleton. May be involved in cellular trafficking of SERT and thereby in regulation of serotonin uptake. {ECO:0000269|PubMed:21638316}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.175
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.927
- hipred
- Y
- hipred_score
- 0.761
- ghis
- 0.641
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gpm6b
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic 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); hearing/vestibular/ear 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); vision/eye phenotype; immune system phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- ossification;nervous system development;protein transport;cell differentiation;positive regulation of bone mineralization;neuron projection development;regulation of actin cytoskeleton organization;negative regulation of serotonin uptake;regulation of focal adhesion assembly;extracellular matrix assembly;negative regulation of protein localization to cell surface
- Cellular component
- plasma membrane;integral component of membrane;membrane raft
- Molecular function
- molecular_function