PCDHA10
Basic information
Region (hg38): 5:140855883-141012347
Previous symbols: [ "CNRS8" ]
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 PCDHA10 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 | 10 | 11 | ||||
| missense | 60 | 66 | ||||
| nonsense | 1 | |||||
| start loss | 1 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 269 | 42 | 312 | |||
| Total | 0 | 0 | 330 | 60 | 2 |
Variants in PCDHA10
This is a list of pathogenic ClinVar variants found in the PCDHA10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PCDHA10 | protein_coding | protein_coding | ENST00000307360 | 4 | 156335 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.09e-14 | 0.0870 | 125002 | 39 | 693 | 125734 | 0.00292 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.756 | 647 | 595 | 1.09 | 0.0000416 | 6079 |
| Missense in Polyphen | 213 | 192.84 | 1.1046 | 2161 | ||
| Synonymous | -0.314 | 297 | 290 | 1.02 | 0.0000245 | 2060 |
| Loss of Function | 0.725 | 23 | 27.1 | 0.850 | 0.00000132 | 325 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00768 | 0.00738 |
| Ashkenazi Jewish | 0.00587 | 0.00517 |
| East Asian | 0.00169 | 0.00163 |
| Finnish | 0.0101 | 0.00961 |
| European (Non-Finnish) | 0.00192 | 0.00177 |
| Middle Eastern | 0.00169 | 0.00163 |
| South Asian | 0.00309 | 0.00294 |
| Other | 0.00248 | 0.00212 |
dbNSFP
Source:
- Function
- FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- 0.925
- rvis_EVS
- 1.61
- rvis_percentile_EVS
- 95.93
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.172
- ghis
- 0.402
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Pcdha9
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;nervous system development
- Cellular component
- extracellular region;integral component of plasma membrane
- Molecular function
- calcium ion binding