SDC3

syndecan 3, the group of Syndecans

Basic information

Region (hg38): 1:30869465-30908758

Links

ENSG00000162512 ∙ NCBI:9672 ∙ OMIM:186357 ∙ HGNC:10660 ∙ Uniprot:O75056 ∙ 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 SDC3 gene.

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.

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				1	1	2
missense			24	1	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2		2	4
Total	0	0	26	2	5

Variants in SDC3

This is a list of pathogenic ClinVar variants found in the SDC3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-30872938-T-A			Benign (Jun 19, 2021)
1-30873045-G-A			Benign (Jun 19, 2021)
1-30873224-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-30873240-GCTT-G			Uncertain significance (Apr 23, 2021)
1-30873260-G-A		not specified	Uncertain significance (Nov 10, 2022)
1-30873281-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-30874359-G-A		not specified	Uncertain significance (Jun 28, 2023)
1-30874365-A-T		not specified	Uncertain significance (Dec 22, 2023)
1-30874392-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-30874398-G-A		not specified	Uncertain significance (Mar 21, 2022)
1-30874440-G-T		not specified	Uncertain significance (Nov 07, 2022)
1-30874473-G-A		Obesity, association with	association (May 01, 2019)
1-30874491-T-G		not specified	Uncertain significance (Jan 26, 2022)
1-30874496-T-C			Likely benign (Jul 17, 2018)
1-30874592-C-A			Benign (Jun 14, 2018)
1-30876560-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-30876598-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-30876623-C-G		not specified	Uncertain significance (Sep 26, 2023)
1-30876637-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-30876659-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-30876731-A-C		not specified	Uncertain significance (Apr 26, 2023)
1-30876736-G-A		not specified	Likely benign (Dec 06, 2022)
1-30876742-G-T		not specified	Uncertain significance (Jan 27, 2022)
1-30876755-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-30876800-C-T		Obesity, association with	association (May 01, 2019)

GnomAD

Source: gnomAD

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: dbNSFP

• 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