SDC4
syndecan 4, the group of Syndecans
Basic information
Region (hg38): 20:45325288-45348424
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 SDC4 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 | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in SDC4
This is a list of pathogenic ClinVar variants found in the SDC4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-45327269-C-T | not specified | Uncertain significance (Mar 18, 2024) | ||
| 20-45327330-T-G | not specified | Uncertain significance (Dec 18, 2023) | ||
| 20-45327349-C-T | not specified | Uncertain significance (Sep 06, 2022) | ||
| 20-45327350-G-A | not specified | Uncertain significance (Dec 15, 2023) | ||
| 20-45327377-C-T | not specified | Uncertain significance (Nov 13, 2023) | ||
| 20-45327403-C-G | not specified | Uncertain significance (Jun 30, 2022) | ||
| 20-45328870-G-A | Type 2 diabetes mellitus | Benign (-) | ||
| 20-45330115-G-A | Type 2 diabetes mellitus | Benign (-) | ||
| 20-45330399-T-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| 20-45330407-A-C | not specified | Uncertain significance (May 27, 2022) | ||
| 20-45330480-C-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 20-45333046-C-T | not specified | Likely benign (Mar 31, 2023) | ||
| 20-45335648-T-C | Type 2 diabetes mellitus | Benign (-) | ||
| 20-45335827-C-G | not specified | Uncertain significance (Aug 30, 2022) | ||
| 20-45335848-C-T | not specified | Uncertain significance (Oct 21, 2021) | ||
| 20-45336885-A-G | Type 2 diabetes mellitus | Benign (-) | ||
| 20-45340366-CT-C | Type 2 diabetes mellitus | Benign (-) | ||
| 20-45348372-G-A | not specified | Uncertain significance (May 22, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SDC4 | protein_coding | protein_coding | ENST00000372733 | 5 | 23137 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00415 | 0.873 | 125729 | 0 | 19 | 125748 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.117 | 118 | 114 | 1.03 | 0.00000624 | 1271 |
| Missense in Polyphen | 39 | 40.43 | 0.96463 | 491 | ||
| Synonymous | 0.0942 | 49 | 49.8 | 0.983 | 0.00000301 | 399 |
| Loss of Function | 1.30 | 5 | 9.29 | 0.538 | 5.66e-7 | 100 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000141 | 0.000141 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413). {ECO:0000269|PubMed:22660413}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Proteoglycans in cancer - 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;Beta3 integrin cell surface interactions;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-4-mediated signaling events;FGF signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.207
Intolerance Scores
- loftool
- 0.572
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.261
- hipred
- Y
- hipred_score
- 0.506
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.861
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sdc4
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; vision/eye phenotype; muscle phenotype; hematopoietic system 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); 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); embryo phenotype; renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- sdc4
- Affected structure
- CaP motoneuron
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- retinoid metabolic process;ureteric bud development;neural tube closure;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;regulation of fibroblast migration;cell migration;wound healing;negative regulation of T cell proliferation;positive regulation of protein kinase activity;leukocyte migration;positive regulation of stress fiber assembly;positive regulation of focal adhesion assembly;inner ear receptor cell stereocilium organization;positive regulation of exosomal secretion;positive regulation of extracellular exosome assembly
- Cellular component
- Golgi lumen;plasma membrane;integral component of plasma membrane;focal adhesion;cell surface;costamere;lysosomal lumen;membrane raft;extracellular exosome
- Molecular function
- fibronectin binding;protein kinase C binding;protein binding;identical protein binding;thrombospondin receptor activity