CRISPLD2
protein-codingcysteine rich secretory protein LCCL domain containing 2
Gene summary
Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Jul 2025]
- LCRISP2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~100.8 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 CRISPLD2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031476.4. 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 | 1 | 11 | 5 | 17 | ||
| missense | 126 | 5 | 3 | 134 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 130 | 16 | 8 | 154 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_113664.1 | 14 | MANE Select | |
| Ensembl | ENSP00000262424.5 | 14 | MANE Select | |
| Ensembl | ENSP00000456952.1 | 7 | Standard | |
| Ensembl | ENSP00000457655.1 | 12 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| crispld2 | Danio rerio | Structure: hypophyseal fenestra Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- extracellular matrix organization
- lung development
- neutrophil degranulation
- face morphogenesis
Molecular Function
- glycosaminoglycan binding
- heparin binding
Cellular Component
- extracellular region
- extracellular space
- transport vesicle
- extracellular matrix
- secretory granule lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262424
- Coding exons
- 14
- Length
- 100785
- Individuals with no LoFs
- 125674
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 73
- Defined
- 125747
- p
- 0.000290
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.60 | 390 | 311 | 1.26 | 0.0000190 | 3252 |
| Missense (PolyPhen) | 148 | 142.13 | 1.0413 | 1409 | ||
| Synonymous | -2.47 | 167 | 131 | 1.27 | 0.00000970 | 917 |
| Loss of Function | 2.17 | 18 | 31.1 | 0.579 | 0.00000141 | 356 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00040 | 0.00037 | rare |
| Latino/Admixed American | 0.00024 | 0.00023 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00026 | 0.00023 | rare |
| European (Non-Finnish) | 0.00040 | 0.00038 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00035 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Promotes matrix assembly. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.235
- RVIS EVS
- 0.45
- RVIS percentile EVS
- 78
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.185
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |