SDC2
syndecan 2, the group of Syndecans|CD molecules
Basic information
Region (hg38): 8:96493813-96611790
Previous symbols: [ "HSPG", "HSPG1" ]
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 SDC2 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 1 |
Variants in SDC2
This is a list of pathogenic ClinVar variants found in the SDC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-96494297-C-T | not specified | Uncertain significance (Jan 06, 2023) | ||
| 8-96593501-A-G | not specified | Uncertain significance (Aug 14, 2023) | ||
| 8-96593508-T-A | not specified | Uncertain significance (Jan 26, 2023) | ||
| 8-96602433-T-A | Benign (Apr 24, 2019) | |||
| 8-96602455-T-G | not specified | Uncertain significance (Aug 16, 2021) | ||
| 8-96602488-C-T | not specified | Uncertain significance (Oct 12, 2022) | ||
| 8-96608444-T-C | not specified | Uncertain significance (May 02, 2024) | ||
| 8-96609391-T-C | not specified | Uncertain significance (Dec 02, 2021) | ||
| 8-96609414-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 8-96609451-G-A | not specified | Uncertain significance (Jul 20, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SDC2 | protein_coding | protein_coding | ENST00000302190 | 5 | 118422 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.405 | 0.587 | 125731 | 0 | 6 | 125737 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.462 | 97 | 111 | 0.876 | 0.00000586 | 1284 |
| Missense in Polyphen | 42 | 57.87 | 0.72577 | 661 | ||
| Synonymous | -0.620 | 48 | 42.8 | 1.12 | 0.00000239 | 396 |
| Loss of Function | 2.23 | 2 | 9.38 | 0.213 | 4.61e-7 | 119 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000354 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Cell surface proteoglycan that bears heparan sulfate. Regulates dendritic arbor morphogenesis (By similarity). {ECO:0000250}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Malaria - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);miRNA targets in ECM and membrane receptors;Developmental Biology;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism of carbohydrates;Post-translational protein phosphorylation;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;Post-translational protein modification;Metabolism of proteins;Extracellular matrix organization;EPH-Ephrin signaling;Metabolism;EPHB-mediated forward signaling;Metabolism of vitamins and cofactors;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Integrin;TGF_beta_Receptor;SHP2 signaling;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;Axon guidance;Visual phototransduction;GPCR downstream signalling;Wnt Canonical;Wnt Mammals;FGF signaling pathway;Syndecan-2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.555
Intolerance Scores
- loftool
- 0.414
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.49
Haploinsufficiency Scores
- pHI
- 0.553
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.554
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.308
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sdc2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype; vision/eye phenotype;
Zebrafish Information Network
- Gene name
- sdc2
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- retinoid metabolic process;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;biological_process;cell migration;post-translational protein modification;cellular protein metabolic process;ephrin receptor signaling pathway;dendrite morphogenesis;regulation of dendrite morphogenesis;leukocyte migration
- Cellular component
- endoplasmic reticulum lumen;Golgi lumen;plasma membrane;cell surface;integral component of membrane;lysosomal lumen;collagen-containing extracellular matrix
- Molecular function
- protein binding;PDZ domain binding;identical protein binding