SCIN
Basic information
Region (hg38): 7:12570577-12660182
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (133 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCIN gene is commonly pathogenic or not. These statistics are base on transcript: NM_001112706.3. 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 | 0 | |||||
| missense | 130 | 133 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 130 | 3 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SCIN | protein_coding | protein_coding | ENST00000297029 | 16 | 83026 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.72e-36 | 7.71e-8 | 124497 | 0 | 141 | 124638 | 0.000566 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.771 | 404 | 363 | 1.11 | 0.0000183 | 4645 |
| Missense in Polyphen | 172 | 157.05 | 1.0952 | 1957 | ||
| Synonymous | -2.13 | 168 | 136 | 1.23 | 0.00000717 | 1326 |
| Loss of Function | -1.71 | 48 | 36.8 | 1.30 | 0.00000173 | 474 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00158 | 0.00143 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000282 | 0.000278 |
| Finnish | 0.000326 | 0.000325 |
| European (Non-Finnish) | 0.000555 | 0.000540 |
| Middle Eastern | 0.000282 | 0.000278 |
| South Asian | 0.00100 | 0.000981 |
| Other | 0.000520 | 0.000496 |
dbNSFP
Source:
- Function
- FUNCTION: Ca(2+)-dependent actin filament-severing protein that has a regulatory function in exocytosis by affecting the organization of the microfilament network underneath the plasma membrane (PubMed:8547642, PubMed:26365202). Severing activity is inhibited by phosphatidylinositol 4,5-bis-phosphate (PIP2) (By similarity). In vitro, also has barbed end capping and nucleating activities in the presence of Ca(2+). Required for megakaryocyte differentiation, maturation, polyploidization and apoptosis with the release of platelet-like particles (PubMed:11568009). Plays a role in osteoclastogenesis (OCG) and actin cytoskeletal organization in osteoclasts (By similarity). Regulates chondrocyte proliferation and differentiation (By similarity). Inhibits cell proliferation and tumorigenesis. Signaling is mediated by MAPK, p38 and JNK pathways (PubMed:11568009). {ECO:0000250|UniProtKB:Q28046, ECO:0000250|UniProtKB:Q5ZIV9, ECO:0000250|UniProtKB:Q60604, ECO:0000269|PubMed:11568009, ECO:0000269|PubMed:26365202, ECO:0000269|PubMed:8547642}.;
- Pathway
- Fc gamma R-mediated phagocytosis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Endochondral Ossification
(Consensus)
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- 0.993
- rvis_EVS
- 1.22
- rvis_percentile_EVS
- 93.24
Haploinsufficiency Scores
- pHI
- 0.497
- hipred
- N
- hipred_score
- 0.449
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.714
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Scin
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- negative regulation of cell population proliferation;calcium ion regulated exocytosis;regulation of chondrocyte differentiation;sequestering of actin monomers;positive regulation of apoptotic process;actin nucleation;positive regulation of megakaryocyte differentiation;actin filament severing;positive regulation of secretion;positive regulation of actin nucleation;actin filament capping
- Cellular component
- podosome;cytoplasm;plasma membrane;brush border;cell cortex;cell junction;cell projection;extracellular exosome
- Molecular function
- phosphatidylserine binding;actin binding;calcium ion binding;1-phosphatidylinositol binding;phosphatidylinositol-4,5-bisphosphate binding;actin filament binding