SDC4

syndecan 4, the group of Syndecans

Basic information

Region (hg38): 20:45325287-45348424

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.

• 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	1		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
20-45327330-T-G		not specified	Uncertain significance (Dec 18, 2023)
20-45327349-C-T		not specified	Uncertain significance (Sep 06, 2022)
20-45327350-G-A		not specified	Uncertain significance (Dec 15, 2023)
20-45327377-C-T		not specified	Uncertain significance (Nov 13, 2023)
20-45327403-C-G		not specified	Uncertain significance (Jun 30, 2022)
20-45328870-G-A		Type 2 diabetes mellitus	Benign (-)
20-45330115-G-A		Type 2 diabetes mellitus	Benign (-)
20-45330399-T-C		not specified	Uncertain significance (Aug 02, 2021)
20-45330407-A-C		not specified	Uncertain significance (May 27, 2022)
20-45330480-C-A		not specified	Uncertain significance (Sep 14, 2022)
20-45333046-C-T		not specified	Likely benign (Mar 31, 2023)
20-45335648-T-C		Type 2 diabetes mellitus	Benign (-)
20-45335827-C-G		not specified	Uncertain significance (Aug 30, 2022)
20-45335848-C-T		not specified	Uncertain significance (Oct 21, 2021)
20-45336885-A-G		Type 2 diabetes mellitus	Benign (-)
20-45340366-CT-C		Type 2 diabetes mellitus	Benign (-)

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