SDC3
Basic information
Region (hg38): 1:30869466-30908758
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (70 variants)
- not_provided (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDC3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014654.4. 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 | 2 | |||||
| missense | 66 | 72 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 66 | 5 | 3 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SDC3 | protein_coding | protein_coding | ENST00000339394 | 5 | 39295 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.415 | 0.578 | 125741 | 1 | 4 | 125746 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.179 | 246 | 254 | 0.968 | 0.0000157 | 2757 |
| Missense in Polyphen | 53 | 55.048 | 0.96279 | 537 | ||
| Synonymous | -1.31 | 133 | 115 | 1.16 | 0.00000780 | 1063 |
| Loss of Function | 2.25 | 2 | 9.48 | 0.211 | 4.00e-7 | 126 |
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) | 0.0000100 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000109 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cell surface proteoglycan that may bear heparan sulfate (By similarity). May have a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. {ECO:0000250, ECO:0000269|PubMed:11527150}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;HS-GAG biosynthesis;HS-GAG degradation;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Extracellular matrix organization;Metabolism;Metabolism of vitamins and cofactors;Integrin;EGFR1;Proteoglycan syndecan-mediated signaling events;Cell surface interactions at the vascular wall;Hemostasis;Retinoid metabolism and transport;Syndecan interactions;Non-integrin membrane-ECM interactions;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling;Wnt Canonical;Wnt Mammals;Syndecan-3-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.318
Intolerance Scores
- loftool
- 0.216
- rvis_EVS
- -0.02
- rvis_percentile_EVS
- 52.25
Haploinsufficiency Scores
- pHI
- 0.202
- hipred
- Y
- hipred_score
- 0.604
- ghis
- 0.507
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.652
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Sdc3
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- sdc3
- Affected structure
- pronephric glomerulus
- Phenotype tag
- abnormal
- Phenotype quality
- lacks parts or has fewer parts of type
Gene ontology
- Biological process
- retinoid metabolic process;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;cell migration;leukocyte migration
- Cellular component
- Golgi lumen;plasma membrane;cell surface;membrane;integral component of membrane;lysosomal lumen;collagen-containing extracellular matrix
- Molecular function
- protein binding;identical protein binding