SDC1

syndecan 1, the group of CD molecules|Syndecans

Basic information

Region (hg38): 2:20200796-20225433

Previous symbols: [ "SDC" ]

Links

ENSG00000115884 ∙ NCBI:6382 ∙ OMIM:186355 ∙ HGNC:10658 ∙ Uniprot:P18827 ∙ 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 SDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDC1 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	1	3
missense			11	1	4	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	5

Variants in SDC1

This is a list of pathogenic ClinVar variants found in the SDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-20202771-C-A		not specified	Uncertain significance (Jan 18, 2023)
2-20203118-C-A		not specified	Uncertain significance (Jan 04, 2022)
2-20203164-C-T		not specified	Likely benign (May 02, 2024)
2-20203178-G-A			Likely benign (Jul 13, 2018)
2-20203195-T-A		not specified	Uncertain significance (Apr 12, 2022)
2-20203203-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-20203850-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-20203864-A-G			Uncertain significance (Mar 30, 2021)
2-20203875-C-T		not specified	Uncertain significance (May 24, 2023)
2-20203887-G-A		not specified	Uncertain significance (Jul 26, 2022)
2-20203904-T-C		not specified	Likely benign (Apr 10, 2023)
2-20203919-T-C		not specified	Uncertain significance (May 21, 2024)
2-20204024-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-20204075-G-T		not specified	Uncertain significance (Apr 12, 2024)
2-20204094-C-T			Benign (Dec 31, 2019)
2-20204128-A-G			Benign (Dec 31, 2019)
2-20204196-C-T			Benign (Dec 31, 2019)
2-20204213-G-A			Benign (Jul 13, 2018)
2-20204220-T-C		not specified	Uncertain significance (Dec 16, 2022)
2-20204237-G-A			Benign (May 25, 2018)
2-20204252-G-A		Long QT syndrome	Likely benign (-)
2-20205363-T-C		not specified	Uncertain significance (Jan 10, 2023)
2-20224830-A-G		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDC1	protein_coding	protein_coding	ENST00000381150	5	24637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00841	0.939	125735	0	6	125741	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0390	172	171	1.01	0.00000956	1951
Missense in Polyphen		66	68.518	0.96325		791
Synonymous	-1.14	93	80.0	1.16	0.00000531	685
Loss of Function	1.67	5	11.0	0.455	5.54e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000439
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. 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);Malaria - 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;Other interleukin signaling;Signaling by Interleukins;Metabolism of carbohydrates;Cytokine Signaling in Immune system;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;Immune System;Metabolism;Fibroblast growth factor-1;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;Beta5 beta6 beta7 and beta8 integrin cell surface interactions;Syndecan-1-mediated signaling events;Wnt Mammals;Integrins in angiogenesis (Consensus)

Recessive Scores

• pRec: 0.513

Intolerance Scores

• loftool: 0.389
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.14

Haploinsufficiency Scores

• pHI: 0.0673
• hipred: Y
• hipred_score: 0.556
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.815

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdc1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; neoplasm; 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); hematopoietic system phenotype

Gene ontology

• Biological process: retinoid metabolic process;ureteric bud development;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;inflammatory response;cell migration;cytokine-mediated signaling pathway;wound healing;odontogenesis;response to hydrogen peroxide;myoblast development;leukocyte migration;response to glucocorticoid;response to cAMP;response to calcium ion;striated muscle cell development;Sertoli cell development;canonical Wnt signaling pathway;positive regulation of exosomal secretion;positive regulation of extracellular exosome assembly
• Cellular component: Golgi lumen;plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;protein-containing complex;lysosomal lumen;extracellular exosome
• Molecular function: protein binding;protein C-terminus binding;identical protein binding