SDC2

syndecan 2, the group of Syndecans|CD molecules

Basic information

Region (hg38): 8:96493812-96611790

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

Links

ENSG00000169439 ∙ NCBI:6383 ∙ OMIM:142460 ∙ HGNC:10659 ∙ Uniprot:P34741 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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		1	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)
8-96609391-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: gnomAD

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: 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

	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