CRISP3
protein-codingcysteine rich secretory protein 3, the group of Cysteine rich secretory protein family
Gene summary
This gene encodes a member of the cysteine-rich secretory protein (CRISP) family within the CRISP, antigen 5 and pathogenesis-related 1 proteins superfamily. The encoded protein has an N-terminal CRISP, antigen 5 and pathogenesis-related 1 proteins domain, a hinge region, and a C-terminal ion channel regulator domain. This protein contains cysteine residues, located in both the N- and C-terminal domains, that form eight disulfide bonds, a distinguishing characteristic of this family. This gene is expressed in the male reproductive tract where it plays a role in sperm function and fertilization, and the female reproductive tract where it plays a role in endometrial receptivity for embryo implantation. This gene is upregulated in certain types of prostate cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CRISP3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006061.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 35 | 3 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 3 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006052.2 | 8 | MANE Select | |
| Ensembl | ENSP00000263045.4 | 8 | MANE Select | |
| RefSeq | NP_001177915.1 | 8 | Standard | |
| RefSeq | NP_001355052.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- defense response
- neutrophil degranulation
- innate immune response
Molecular Function
- molecular_function
Cellular Component
- extracellular region
- extracellular space
- extracellular matrix
- specific granule lumen
- specific granule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000433368
- Coding exons
- 8
- Length
- 17054
- Individuals with no LoFs
- 125650
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 54
- Defined
- 125704
- p
- 0.000215
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.379 | 150 | 138 | 1.09 | 0.00000637 | 1758 |
| Missense (PolyPhen) | 31 | 38.448 | 0.80628 | 490 | ||
| Synonymous | -0.981 | 60 | 51.1 | 1.17 | 0.00000271 | 470 |
| Loss of Function | 1.23 | 11 | 16.4 | 0.672 | 8.54e-7 | 181 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000098 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00022 | 0.00020 | rare |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00040 | 0.00040 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- LoFtool
- 0.921
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63.2
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.523
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |