CRISP2
Basic information
Region (hg38): 6:49692358-49713590
Previous symbols: [ "GAPDL5", "TPX1" ]
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 CRISP2 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 | 1 | |||||
| missense | 21 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 21 | 2 | 0 |
Variants in CRISP2
This is a list of pathogenic ClinVar variants found in the CRISP2 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 |
|---|---|---|---|---|---|
| CRISP2 | protein_coding | protein_coding | ENST00000339139 | 7 | 21202 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.44e-12 | 0.0143 | 125634 | 0 | 103 | 125737 | 0.000410 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.456 | 143 | 128 | 1.11 | 0.00000629 | 1591 |
| Missense in Polyphen | 59 | 51.783 | 1.1394 | 633 | ||
| Synonymous | 0.301 | 46 | 48.7 | 0.945 | 0.00000269 | 433 |
| Loss of Function | -0.488 | 17 | 15.0 | 1.14 | 7.32e-7 | 173 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00340 | 0.00339 |
| Ashkenazi Jewish | 0.000809 | 0.000794 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000212 | 0.000211 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000165 | 0.000163 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May regulate some ion channels' activity and therebye regulate calcium fluxes during sperm capacitation. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0644
Intolerance Scores
- loftool
- 0.984
- rvis_EVS
- 0.95
- rvis_percentile_EVS
- 90.01
Haploinsufficiency Scores
- pHI
- 0.246
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.254
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Crisp2
- Phenotype
Gene ontology
- Biological process
- Cellular component
- extracellular space
- Molecular function