SCAMP2
Basic information
Region (hg38): 15:74843729-74873365
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 SCAMP2 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 | 0 | |||||
missense | 16 | 17 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 16 | 1 | 0 |
Variants in SCAMP2
This is a list of pathogenic ClinVar variants found in the SCAMP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-74845087-T-C | not specified | Uncertain significance (Sep 29, 2023) | ||
15-74845198-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
15-74845474-C-T | not specified | Uncertain significance (Dec 17, 2023) | ||
15-74845567-A-G | not specified | Uncertain significance (Jan 18, 2023) | ||
15-74848613-C-G | not specified | Uncertain significance (Nov 17, 2023) | ||
15-74848697-C-T | not specified | Uncertain significance (Aug 10, 2021) | ||
15-74851386-G-A | not specified | Uncertain significance (Mar 16, 2022) | ||
15-74851442-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
15-74852101-C-T | not specified | Uncertain significance (Dec 07, 2021) | ||
15-74852122-G-C | not specified | Uncertain significance (Dec 16, 2023) | ||
15-74852183-C-T | not specified | Uncertain significance (Mar 24, 2023) | ||
15-74854038-T-A | Likely benign (Jan 01, 2023) | |||
15-74854040-G-C | not specified | Uncertain significance (Apr 24, 2024) | ||
15-74854064-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
15-74854594-T-C | not specified | Uncertain significance (Aug 30, 2022) | ||
15-74854603-G-T | not specified | Uncertain significance (Jul 14, 2023) | ||
15-74854632-C-G | not specified | Uncertain significance (May 03, 2023) | ||
15-74854648-T-A | not specified | Uncertain significance (Apr 05, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SCAMP2 | protein_coding | protein_coding | ENST00000268099 | 9 | 29636 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.160 | 0.839 | 125732 | 0 | 13 | 125745 | 0.0000517 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.30 | 130 | 179 | 0.727 | 0.00000970 | 2124 |
Missense in Polyphen | 34 | 54.736 | 0.62116 | 671 | ||
Synonymous | 0.185 | 73 | 75.0 | 0.973 | 0.00000429 | 667 |
Loss of Function | 3.00 | 5 | 19.2 | 0.261 | 9.93e-7 | 195 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000797 | 0.0000791 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.;
- Pathway
- Serotonin Transporter Activity;Monoamine Transport;Arf6 trafficking events
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.272
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.35
Haploinsufficiency Scores
- pHI
- 0.223
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.519
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.876
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scamp2
- Phenotype
Gene ontology
- Biological process
- post-Golgi vesicle-mediated transport;protein transport
- Cellular component
- Golgi membrane;Golgi apparatus;integral component of membrane;transport vesicle;trans-Golgi network membrane;intracellular membrane-bounded organelle;recycling endosome membrane;extracellular exosome
- Molecular function
- protein binding