SOSTDC1
sclerostin domain containing 1, the group of DAN family
Basic information
Region (hg38): 7:16461481-16530580
Links
Phenotypes
GenCC
Source:
No genCC data.
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 SOSTDC1 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 | 2 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 5 |
Variants in SOSTDC1
This is a list of pathogenic ClinVar variants found in the SOSTDC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-16462576-CT-C | Benign/Likely benign (Oct 01, 2024) | |||
| 7-16462589-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 7-16462606-A-G | not specified | Likely benign (Dec 03, 2024) | ||
| 7-16462624-A-G | not specified | Uncertain significance (Sep 03, 2024) | ||
| 7-16462639-T-C | Benign (Jan 08, 2018) | |||
| 7-16462707-G-C | Benign (Jul 13, 2018) | |||
| 7-16462765-T-C | Benign (Sep 01, 2024) | |||
| 7-16462820-C-G | not specified | Uncertain significance (Jul 23, 2024) | ||
| 7-16462821-T-C | Benign (Apr 20, 2018) | |||
| 7-16462835-T-C | not specified | Uncertain significance (Mar 06, 2023) | ||
| 7-16462906-T-C | not specified | Uncertain significance (Dec 13, 2023) | ||
| 7-16462930-G-C | not specified | Uncertain significance (Nov 12, 2021) | ||
| 7-16462951-A-G | not specified | Uncertain significance (Jun 26, 2024) | ||
| 7-16465469-C-T | not specified | Uncertain significance (Jul 02, 2024) | ||
| 7-16465565-T-C | not specified | Uncertain significance (Apr 11, 2023) | ||
| 7-16527002-T-G | not specified | Uncertain significance (Nov 07, 2024) | ||
| 7-16527028-C-A | not specified | Uncertain significance (Nov 14, 2023) | ||
| 7-16527040-C-T | not specified | Uncertain significance (Sep 14, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SOSTDC1 | protein_coding | protein_coding | ENST00000307068 | 2 | 69100 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.163 | 0.779 | 125739 | 0 | 6 | 125745 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.661 | 98 | 118 | 0.829 | 0.00000670 | 1351 |
| Missense in Polyphen | 41 | 64.328 | 0.63736 | 691 | ||
| Synonymous | -0.781 | 48 | 41.6 | 1.15 | 0.00000201 | 393 |
| Loss of Function | 1.56 | 2 | 6.19 | 0.323 | 2.64e-7 | 85 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in the onset of endometrial receptivity for implantation/sensitization for the decidual cell reaction Enhances Wnt signaling and inhibits TGF-beta signaling (By similarity). Directly antagonizes activity of BMP2, BMP4, BMP6 and BMP7 in a dose-dependent manner. {ECO:0000250, ECO:0000269|PubMed:15020244}.;
- Pathway
- Vitamin D Receptor Pathway;EDA Signalling in Hair Follicle Development;BMP receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.158
Intolerance Scores
- loftool
- 0.289
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.95
Haploinsufficiency Scores
- pHI
- 0.200
- hipred
- Y
- hipred_score
- 0.510
- ghis
- 0.456
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.822
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sostdc1
- Phenotype
- growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype;
Gene ontology
- Biological process
- pattern specification process;negative regulation of cell fate commitment;Wnt signaling pathway;negative regulation of Wnt signaling pathway;BMP signaling pathway;negative regulation of BMP signaling pathway;hair follicle morphogenesis;odontogenesis of dentin-containing tooth;negative regulation of myoblast differentiation;mammary gland bud morphogenesis;negative regulation of canonical Wnt signaling pathway;negative regulation of determination of dorsal identity
- Cellular component
- extracellular space
- Molecular function
- BMP binding;BMP receptor activity