SCAMP5
Basic information
Region (hg38): 15:74957219-75021495
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AD
- epilepsy (Limited), mode of inheritance: AR
- complex neurodevelopmental disorder (Moderate), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (13 variants)
- not_provided (11 variants)
- SCAMP5-related_disorder (1 variants)
- Macrocephaly-developmental_delay_syndrome (1 variants)
- SCAMP5-related_neurodevelopmental_disorder_with_autistic_features_and_seizures (1 variants)
- SCAMP5-related_neurodevelopmental_and_movement_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138967.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 15 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 1 | 16 | 3 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SCAMP5 | protein_coding | protein_coding | ENST00000361900 | 6 | 64278 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.651 | 0.348 | 124623 | 0 | 2 | 124625 | 0.00000802 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.05 | 75 | 144 | 0.520 | 0.00000842 | 1562 |
| Missense in Polyphen | 28 | 64.964 | 0.43101 | 704 | ||
| Synonymous | -0.864 | 68 | 59.5 | 1.14 | 0.00000429 | 439 |
| Loss of Function | 2.68 | 2 | 12.0 | 0.166 | 5.16e-7 | 123 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000435 | 0.0000435 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000885 | 0.00000885 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for the calcium-dependent exocytosis of signal sequence-containing cytokines such as CCL5. Probably acts in cooperation with the SNARE machinery. May play a role in accumulation of expanded polyglutamine (polyQ) protein huntingtin (HTT) in case of endoplasmic reticulum stress by inhibiting the endocytosis pathway. {ECO:0000269|PubMed:19234194}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.563
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.437
- hipred
- Y
- hipred_score
- 0.651
- ghis
- 0.706
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.458
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scamp5
- Phenotype
Gene ontology
- Biological process
- exocytosis;protein transport;response to endoplasmic reticulum stress;negative regulation of endocytosis;positive regulation of calcium ion-dependent exocytosis;positive regulation of cytokine secretion
- Cellular component
- Golgi membrane;Golgi apparatus;plasma membrane;integral component of membrane;cell junction;synaptic vesicle membrane;trans-Golgi network membrane;recycling endosome membrane
- Molecular function
- protein binding;protein-containing complex binding