GPC5
Basic information
Region (hg38): 13:91398621-92873682
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (85 variants)
- not_provided (5 variants)
- GPC5-related_disorder (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPC5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004466.6. 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 | 3 | |||||
missense | 81 | 89 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 81 | 8 | 3 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GPC5 | protein_coding | protein_coding | ENST00000377067 | 8 | 1468562 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.99e-10 | 0.550 | 125673 | 0 | 75 | 125748 | 0.000298 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.589 | 351 | 321 | 1.09 | 0.0000168 | 3738 |
Missense in Polyphen | 127 | 119.51 | 1.0626 | 1480 | ||
Synonymous | -1.44 | 143 | 123 | 1.17 | 0.00000680 | 1125 |
Loss of Function | 1.24 | 18 | 24.6 | 0.730 | 0.00000126 | 286 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00120 | 0.00107 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000273 | 0.000272 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000235 | 0.000229 |
Middle Eastern | 0.000273 | 0.000272 |
South Asian | 0.000726 | 0.000719 |
Other | 0.000350 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Cell surface proteoglycan that bears heparan sulfate. {ECO:0000250}.;
- Pathway
- Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;HS-GAG biosynthesis;HS-GAG degradation;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism;Release of Hh-Np from the secreting cell;Hedgehog ligand biogenesis;Metabolism of vitamins and cofactors;Signaling by Hedgehog;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.153
Intolerance Scores
- loftool
- 0.844
- rvis_EVS
- -0.82
- rvis_percentile_EVS
- 11.94
Haploinsufficiency Scores
- pHI
- 0.673
- hipred
- N
- hipred_score
- 0.334
- ghis
- 0.565
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0980
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gpc5
- Phenotype
- homeostasis/metabolism phenotype; skeleton phenotype;
Gene ontology
- Biological process
- retinoid metabolic process;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;regulation of signal transduction
- Cellular component
- extracellular region;extracellular space;Golgi lumen;plasma membrane;integral component of membrane;lysosomal lumen;anchored component of plasma membrane;collagen-containing extracellular matrix
- Molecular function