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SDC1

syndecan 1, the group of CD molecules|Syndecans

Basic information

Region (hg38): 2:20200796-20225433

Previous symbols: [ "SDC" ]

Links

ENSG00000115884NCBI:6382OMIM:186355HGNC:10658Uniprot:P18827AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDC1 gene.

  • Inborn genetic diseases (10 variants)
  • not provided (7 variants)

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
clinvar
1
clinvar
1
clinvar
3
missense
9
clinvar
1
clinvar
4
clinvar
14
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 10 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 Inborn genetic diseases Uncertain significance (Jan 18, 2023)2476395
2-20203118-C-A Inborn genetic diseases Uncertain significance (Jan 04, 2022)2269432
2-20203178-G-A Likely benign (Jul 13, 2018)729993
2-20203195-T-A Inborn genetic diseases Uncertain significance (Apr 12, 2022)2283256
2-20203203-G-A Inborn genetic diseases Uncertain significance (Dec 21, 2022)2353731
2-20203864-A-G Uncertain significance (Mar 30, 2021)626010
2-20203875-C-T Inborn genetic diseases Uncertain significance (May 24, 2023)2560130
2-20203887-G-A Inborn genetic diseases Uncertain significance (Jul 26, 2022)2303134
2-20203904-T-C Inborn genetic diseases Likely benign (Apr 10, 2023)2535670
2-20204024-G-A Inborn genetic diseases Uncertain significance (Feb 10, 2022)2378009
2-20204094-C-T Benign (Dec 31, 2019)742271
2-20204128-A-G Benign (Dec 31, 2019)773122
2-20204196-C-T Benign (Dec 31, 2019)716280
2-20204213-G-A Benign (Jul 13, 2018)720907
2-20204220-T-C Inborn genetic diseases Uncertain significance (Dec 16, 2022)2204501
2-20204237-G-A Benign (May 25, 2018)790815
2-20204252-G-A Long QT syndrome Likely benign (-)207901
2-20205363-T-C Inborn genetic diseases Uncertain significance (Jan 10, 2023)2470757

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDC1protein_codingprotein_codingENST00000381150 524637
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.008410.939125735061257410.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.03901721711.010.000009561951
Missense in Polyphen6668.5180.96325791
Synonymous-1.149380.01.160.00000531685
Loss of Function1.67511.00.4555.54e-7132

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.000.00
European (Non-Finnish)0.00004460.0000439
Middle Eastern0.00005450.0000544
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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