SDC4

syndecan 4, the group of Syndecans

Basic information

Region (hg38): 20:45325288-45348424

Links

ENSG00000124145

∙ NCBI:6385 ∙ OMIM:600017 ∙ HGNC:10661 ∙ Uniprot:P31431 ∙ 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 SDC4 gene.

not_specified (21 variants)
Type_2_diabetes_mellitus (2 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. These statistics are base on transcript: NM_000002999.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			20 clinvar	1 clinvar		21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDC4	protein_coding	protein_coding	ENST00000372733	5	23137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00415	0.873	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.117	118	114	1.03	0.00000624	1271
Missense in Polyphen		39	40.43	0.96463		491
Synonymous	0.0942	49	49.8	0.983	0.00000301	399
Loss of Function	1.30	5	9.29	0.538	5.66e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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