SMOC2
Basic information
Region (hg38): 6:168441151-168673445
Links
Phenotypes
GenCC
Source:
- dentin dysplasia type I (Strong), mode of inheritance: AR
- atypical dentin dysplasia due to SMOC2 deficiency (Supportive), mode of inheritance: AR
- dentin dysplasia type I (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Dentin dysplasia, type I | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Dental | 22152679; 23317772 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (2 variants)
- DENTIN DYSPLASIA, TYPE I, WITH EXTREME MICRODONTIA AND MISSHAPEN TEETH (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMOC2 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 | 10 | 17 | ||||
missense | 61 | 64 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 4 | 5 | |||
non coding | 28 | 31 | ||||
Total | 2 | 1 | 61 | 14 | 37 |
Variants in SMOC2
This is a list of pathogenic ClinVar variants found in the SMOC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-168441267-C-T | Benign (Jun 19, 2021) | |||
6-168441334-A-G | Benign (Jun 19, 2021) | |||
6-168441383-C-T | Pathogenic (Mar 20, 2023) | |||
6-168441422-C-G | not specified | Uncertain significance (Aug 08, 2023) | ||
6-168441427-G-T | Likely benign (Nov 29, 2022) | |||
6-168441430-C-G | SMOC2-related disorder | Likely benign (Jul 29, 2022) | ||
6-168441432-C-A | not specified | Uncertain significance (Sep 04, 2024) | ||
6-168441433-T-G | Benign (Jan 29, 2024) | |||
6-168441447-C-T | not specified | Uncertain significance (May 23, 2023) | ||
6-168441455-G-T | DENTIN DYSPLASIA, TYPE I, WITH EXTREME MICRODONTIA AND MISSHAPEN TEETH | Pathogenic (Oct 01, 2017) | ||
6-168509763-C-G | Benign (Nov 12, 2018) | |||
6-168509898-T-C | Benign (Jun 30, 2024) | |||
6-168509964-C-T | Uncertain significance (Dec 19, 2021) | |||
6-168509966-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
6-168509970-C-T | not specified | Uncertain significance (Feb 23, 2023) | ||
6-168509982-C-T | not specified | Uncertain significance (Apr 20, 2024) | ||
6-168510017-C-T | Uncertain significance (Apr 25, 2022) | |||
6-168510033-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
6-168510063-T-C | not specified | Uncertain significance (Dec 03, 2021) | ||
6-168510072-G-A | not specified | Uncertain significance (Apr 17, 2023) | ||
6-168510073-A-G | Likely benign (Oct 04, 2023) | |||
6-168510084-A-C | not specified | Uncertain significance (Jun 17, 2024) | ||
6-168510340-T-A | Benign (Nov 12, 2018) | |||
6-168526105-G-A | Benign (Nov 12, 2018) | |||
6-168526358-G-A | Uncertain significance (May 31, 2017) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SMOC2 | protein_coding | protein_coding | ENST00000354536 | 13 | 232154 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00253 | 0.997 | 125723 | 0 | 25 | 125748 | 0.0000994 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.642 | 254 | 284 | 0.893 | 0.0000186 | 2956 |
Missense in Polyphen | 72 | 97.044 | 0.74193 | 900 | ||
Synonymous | 0.0349 | 122 | 122 | 0.996 | 0.00000912 | 859 |
Loss of Function | 3.00 | 9 | 25.3 | 0.356 | 0.00000107 | 318 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000182 | 0.000181 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000133 | 0.000132 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000983 | 0.0000980 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Promotes matrix assembly and cell adhesiveness (By similarity). Can stimulate endothelial cell proliferation, migration, as well as angiogenesis. {ECO:0000250, ECO:0000269|PubMed:16774925}.;
- Disease
- DISEASE: Dentin dysplasia 1 (DTDP1) [MIM:125400]: A dental defect in which both primary and secondary dentitions are affected. The clinical crowns of both permanent and deciduous teeth are of normal shape, form and color in most cases, although they may be slightly opalescent and blue or brown. Teeth may be very mobile and exfoliate spontaneously because of inadequate root formation. On radiographs, the roots are short and may be more pointed than normal. Pulp chambers are usually absent except for a chevron- shaped remnant in the crown. Root canals are usually absent. {ECO:0000269|PubMed:22152679}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Gastric Cancer Network 1
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.696
- rvis_EVS
- -0.53
- rvis_percentile_EVS
- 20.82
Haploinsufficiency Scores
- pHI
- 0.0972
- hipred
- Y
- hipred_score
- 0.604
- ghis
- 0.520
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.793
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Smoc2
- Phenotype
- craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; digestive/alimentary phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- smoc2
- Affected structure
- neutrophil
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- positive regulation of endothelial cell migration;positive regulation of cell-substrate adhesion;extracellular matrix organization;positive regulation of vascular wound healing;positive regulation of fibroblast growth factor receptor signaling pathway;positive regulation of angiogenesis;positive regulation of mitotic cell cycle;positive regulation of vascular endothelial growth factor signaling pathway;positive regulation of DNA biosynthetic process;positive regulation of endothelial cell chemotaxis
- Cellular component
- basement membrane;interstitial matrix;extracellular space;cell periphery
- Molecular function
- calcium ion binding;heparin binding