SCAMP3
secretory carrier membrane protein 3, the group of Secretory carrier membrane proteins
Basic information
Region (hg38): 1:155255978-155262430
Previous symbols: [ "C1orf3" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (13 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP3 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in SCAMP3
This is a list of pathogenic ClinVar variants found in the SCAMP3 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-155256283-C-T | Inborn genetic diseases | Uncertain significance (Jan 10, 2023) | ||
| 1-155256328-G-A | Inborn genetic diseases | Uncertain significance (Oct 03, 2022) | ||
| 1-155256395-C-T | Inborn genetic diseases | Uncertain significance (Jan 26, 2022) | ||
| 1-155256400-C-T | Inborn genetic diseases | Uncertain significance (Feb 27, 2023) | ||
| 1-155256413-A-C | Inborn genetic diseases | Uncertain significance (Nov 16, 2021) | ||
| 1-155256676-G-A | Inborn genetic diseases | Uncertain significance (Dec 15, 2022) | ||
| 1-155256723-G-A | Inborn genetic diseases | Uncertain significance (Aug 08, 2022) | ||
| 1-155256724-C-T | Inborn genetic diseases | Uncertain significance (Aug 12, 2021) | ||
| 1-155256732-A-G | Inborn genetic diseases | Uncertain significance (Jan 26, 2022) | ||
| 1-155257627-A-T | Inborn genetic diseases | Uncertain significance (Nov 03, 2022) | ||
| 1-155258889-T-A | Inborn genetic diseases | Uncertain significance (May 17, 2023) | ||
| 1-155258928-G-A | Inborn genetic diseases | Uncertain significance (Dec 13, 2022) | ||
| 1-155260366-G-C | Inborn genetic diseases | Uncertain significance (Nov 12, 2021) | ||
| 1-155260441-C-G | Inborn genetic diseases | Uncertain significance (Apr 18, 2023) | ||
| 1-155260565-G-A | Inborn genetic diseases | Uncertain significance (Aug 13, 2021) | ||
| 1-155260595-T-G | Inborn genetic diseases | Uncertain significance (Jun 03, 2022) | ||
| 1-155261731-G-A | Inborn genetic diseases | Uncertain significance (Oct 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SCAMP3 | protein_coding | protein_coding | ENST00000302631 | 9 | 6452 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00219 | 0.994 | 125707 | 0 | 41 | 125748 | 0.000163 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.381 | 188 | 203 | 0.925 | 0.0000112 | 2230 |
| Missense in Polyphen | 64 | 76.91 | 0.83214 | 889 | ||
| Synonymous | 0.159 | 80 | 81.8 | 0.978 | 0.00000455 | 714 |
| Loss of Function | 2.55 | 8 | 20.5 | 0.391 | 0.00000111 | 203 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000560 | 0.000560 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000561 | 0.0000544 |
| Finnish | 0.0000939 | 0.0000924 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.0000561 | 0.0000544 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.000489 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.;
- Pathway
- Fibroblast growth factor-1;EGFR1
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.742
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.92
Haploinsufficiency Scores
- pHI
- 0.206
- hipred
- Y
- hipred_score
- 0.722
- ghis
- 0.536
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.927
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scamp3
- Phenotype
Gene ontology
- Biological process
- post-Golgi vesicle-mediated transport;protein transport
- Cellular component
- Golgi membrane;Golgi apparatus;integral component of membrane;trans-Golgi network membrane;intracellular membrane-bounded organelle;recycling endosome membrane;extracellular exosome
- Molecular function
- ubiquitin protein ligase binding