PCDHB1
Basic information
Region (hg38): 5:141051374-141059346
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 PCDHB1 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 | 55 | 58 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 55 | 3 | 0 |
Variants in PCDHB1
This is a list of pathogenic ClinVar variants found in the PCDHB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-141051484-G-A | not specified | Uncertain significance (Mar 08, 2025) | ||
| 5-141051510-G-A | not specified | Uncertain significance (Feb 25, 2025) | ||
| 5-141051525-A-T | not specified | Uncertain significance (Jul 27, 2024) | ||
| 5-141051529-T-C | not specified | Uncertain significance (May 03, 2023) | ||
| 5-141051562-T-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 5-141051586-T-C | not specified | Uncertain significance (May 11, 2022) | ||
| 5-141051595-G-C | not specified | Uncertain significance (Feb 26, 2024) | ||
| 5-141051685-A-G | not specified | Uncertain significance (Apr 07, 2023) | ||
| 5-141051733-A-C | not specified | Uncertain significance (Sep 13, 2023) | ||
| 5-141051738-C-G | not specified | Uncertain significance (Dec 24, 2024) | ||
| 5-141051771-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 5-141051780-C-A | not specified | Uncertain significance (Feb 26, 2025) | ||
| 5-141051823-G-A | not specified | Uncertain significance (Nov 11, 2024) | ||
| 5-141051843-G-T | not specified | Uncertain significance (Feb 12, 2025) | ||
| 5-141051852-G-T | not specified | Uncertain significance (Aug 14, 2023) | ||
| 5-141051877-A-G | not specified | Uncertain significance (Mar 29, 2024) | ||
| 5-141051881-G-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 5-141052011-C-T | not specified | Uncertain significance (Jun 30, 2022) | ||
| 5-141052044-G-T | not specified | Uncertain significance (Feb 07, 2025) | ||
| 5-141052184-C-A | not specified | Uncertain significance (Sep 29, 2022) | ||
| 5-141052240-A-G | not specified | Uncertain significance (Jul 27, 2024) | ||
| 5-141052249-T-C | not specified | Uncertain significance (Dec 14, 2022) | ||
| 5-141052279-A-G | not specified | Uncertain significance (Jun 21, 2023) | ||
| 5-141052297-C-T | not specified | Uncertain significance (Feb 19, 2025) | ||
| 5-141052342-C-T | not specified | Uncertain significance (Jan 09, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PCDHB1 | protein_coding | protein_coding | ENST00000306549 | 1 | 2534 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 7.53e-11 | 0.139 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.02 | 384 | 445 | 0.863 | 0.0000236 | 5331 |
| Missense in Polyphen | 171 | 192.3 | 0.88921 | 2390 | ||
| Synonymous | -0.209 | 191 | 187 | 1.02 | 0.0000109 | 1735 |
| Loss of Function | 0.515 | 17 | 19.5 | 0.874 | 0.00000114 | 253 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
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.;
Intolerance Scores
- loftool
- 0.876
- rvis_EVS
- 0.56
- rvis_percentile_EVS
- 81.63
Haploinsufficiency Scores
- pHI
- 0.217
- hipred
- N
- hipred_score
- 0.367
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.233
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pcdhb1
- Phenotype
Gene ontology
- Biological process
- cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules
- Cellular component
- integral component of plasma membrane
- Molecular function
- calcium ion binding