Menu
GeneBe

SDC2

syndecan 2, the group of Syndecans|CD molecules

Basic information

Region (hg38): 8:96493812-96611790

Previous symbols: [ "HSPG", "HSPG1" ]

Links

ENSG00000169439NCBI:6383OMIM:142460HGNC:10659Uniprot:P34741AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDC2 gene.

  • Inborn genetic diseases (8 variants)
  • not provided (1 variants)

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
8
clinvar
1
clinvar
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 Inborn genetic diseases Uncertain significance (Jan 06, 2023)2474331
8-96593501-A-G Inborn genetic diseases Uncertain significance (Aug 14, 2023)2618436
8-96593508-T-A Inborn genetic diseases Uncertain significance (Jan 26, 2023)2468606
8-96602433-T-A Benign (Apr 24, 2019)1288543
8-96602455-T-G Inborn genetic diseases Uncertain significance (Aug 16, 2021)2245641
8-96602488-C-T Inborn genetic diseases Uncertain significance (Oct 12, 2022)2372584
8-96609391-T-C Inborn genetic diseases Uncertain significance (Dec 02, 2021)2395107
8-96609414-C-T Inborn genetic diseases Uncertain significance (Jul 12, 2023)2595365
8-96609451-G-A Inborn genetic diseases Uncertain significance (Jul 20, 2021)2238609

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDC2protein_codingprotein_codingENST00000302190 5118422
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4050.587125731061257370.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.462971110.8760.000005861284
Missense in Polyphen4257.870.72577661
Synonymous-0.6204842.81.120.00000239396
Loss of Function2.2329.380.2134.61e-7119

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00003540.0000352
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0001640.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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