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GeneBe

SDC3

syndecan 3, the group of Syndecans

Basic information

Region (hg38): 1:30869465-30908758

Links

ENSG00000162512NCBI:9672OMIM:186357HGNC:10660Uniprot:O75056AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDC3 gene.

  • Inborn genetic diseases (20 variants)
  • not provided (7 variants)

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
clinvar
1
clinvar
2
missense
18
clinvar
1
clinvar
2
clinvar
21
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
2
clinvar
3
Total 0 0 19 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)1287484
1-30873045-G-A Benign (Jun 19, 2021)1289937
1-30873224-T-C Inborn genetic diseases Uncertain significance (Jan 10, 2023)2474736
1-30873240-GCTT-G Uncertain significance (Apr 23, 2021)1334719
1-30873260-G-A Inborn genetic diseases Uncertain significance (Nov 10, 2022)2268029
1-30874359-G-A Inborn genetic diseases Uncertain significance (Jun 28, 2023)2593355
1-30874392-G-A Inborn genetic diseases Uncertain significance (Dec 07, 2021)2265454
1-30874398-G-A Inborn genetic diseases Uncertain significance (Mar 21, 2022)2386793
1-30874440-G-T Inborn genetic diseases Uncertain significance (Nov 07, 2022)2322766
1-30874473-G-A Obesity, association with association (May 01, 2019)12755
1-30874491-T-G Inborn genetic diseases Uncertain significance (Jan 26, 2022)2404766
1-30874496-T-C Likely benign (Jul 17, 2018)760302
1-30874592-C-A Benign (Jun 14, 2018)737823
1-30876560-C-T Inborn genetic diseases Uncertain significance (Feb 10, 2022)2227388
1-30876637-G-A Inborn genetic diseases Uncertain significance (Jan 04, 2022)2208181
1-30876659-G-A Inborn genetic diseases Uncertain significance (Feb 06, 2023)2462778
1-30876731-A-C Inborn genetic diseases Uncertain significance (Apr 26, 2023)2541023
1-30876736-G-A Inborn genetic diseases Likely benign (Dec 06, 2022)2411583
1-30876742-G-T Inborn genetic diseases Uncertain significance (Jan 27, 2022)2365683
1-30876755-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2023)2615706
1-30876800-C-T Obesity, association with association (May 01, 2019)12756
1-30876824-T-C Inborn genetic diseases Uncertain significance (May 27, 2022)2292513
1-30876830-C-T Benign (May 31, 2018)722531
1-30876856-C-T Inborn genetic diseases Uncertain significance (Aug 16, 2022)2399198
1-30876866-C-T Inborn genetic diseases Uncertain significance (Dec 06, 2022)2216417

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDC3protein_codingprotein_codingENST00000339394 539295
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4150.578125741141257460.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1792462540.9680.00001572757
Missense in Polyphen5355.0480.96279537
Synonymous-1.311331151.160.000007801063
Loss of Function2.2529.480.2114.00e-7126

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00001000.00000879
Middle Eastern0.00005440.0000544
South Asian0.0001090.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh

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