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GeneBe

SDC4

syndecan 4, the group of Syndecans

Basic information

Region (hg38): 20:45325287-45348424

Links

ENSG00000124145NCBI:6385OMIM:600017HGNC:10661Uniprot:P31431AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDC4 gene.

  • Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDC4 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
7
clinvar
1
clinvar
8
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 7 1 0

Variants in SDC4

This is a list of pathogenic ClinVar variants found in the SDC4 region.

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

Position Type Phenotype Significance ClinVar
20-45327349-C-T Inborn genetic diseases Uncertain significance (Sep 06, 2022)2346544
20-45327403-C-G Inborn genetic diseases Uncertain significance (Jun 30, 2022)2299643
20-45328870-G-A Type 2 diabetes mellitus Benign (-)444106
20-45330115-G-A Type 2 diabetes mellitus Benign (-)444111
20-45330399-T-C Inborn genetic diseases Uncertain significance (Aug 02, 2021)2373597
20-45330407-A-C Inborn genetic diseases Uncertain significance (May 27, 2022)2354835
20-45330480-C-A Inborn genetic diseases Uncertain significance (Sep 14, 2022)2311728
20-45333046-C-T Inborn genetic diseases Likely benign (Mar 31, 2023)2531870
20-45335648-T-C Type 2 diabetes mellitus Benign (-)444113
20-45335827-C-G Inborn genetic diseases Uncertain significance (Aug 30, 2022)2309577
20-45335848-C-T Inborn genetic diseases Uncertain significance (Oct 21, 2021)2256296
20-45336885-A-G Type 2 diabetes mellitus Benign (-)444109
20-45340366-CT-C Type 2 diabetes mellitus Benign (-)444115

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDC4protein_codingprotein_codingENST00000372733 523137
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.004150.8731257290191257480.0000756
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1171181141.030.000006241271
Missense in Polyphen3940.430.96463491
Synonymous0.09424949.80.9830.00000301399
Loss of Function1.3059.290.5385.66e-7100

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006160.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001410.000141
Middle Eastern0.000.00
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413). {ECO:0000269|PubMed:22660413}.;
Pathway
Cell adhesion molecules (CAMs) - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Proteoglycans in cancer - 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;Beta3 integrin cell surface interactions;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-4-mediated signaling events;FGF signaling pathway (Consensus)

Recessive Scores

pRec
0.207

Intolerance Scores

loftool
0.572
rvis_EVS
-0.16
rvis_percentile_EVS
41.64

Haploinsufficiency Scores

pHI
0.261
hipred
Y
hipred_score
0.506
ghis
0.505

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.861

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sdc4
Phenotype
homeostasis/metabolism phenotype; cellular phenotype; vision/eye phenotype; muscle phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; renal/urinary system phenotype;

Zebrafish Information Network

Gene name
sdc4
Affected structure
CaP motoneuron
Phenotype tag
abnormal
Phenotype quality
morphology

Gene ontology

Biological process
retinoid metabolic process;ureteric bud development;neural tube closure;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;regulation of fibroblast migration;cell migration;wound healing;negative regulation of T cell proliferation;positive regulation of protein kinase activity;leukocyte migration;positive regulation of stress fiber assembly;positive regulation of focal adhesion assembly;inner ear receptor cell stereocilium organization;positive regulation of exosomal secretion;positive regulation of extracellular exosome assembly
Cellular component
Golgi lumen;plasma membrane;integral component of plasma membrane;focal adhesion;cell surface;costamere;lysosomal lumen;membrane raft;extracellular exosome
Molecular function
fibronectin binding;protein kinase C binding;protein binding;identical protein binding;thrombospondin receptor activity