Menu
GeneBe

SDCBP

syndecan binding protein, the group of PDZ domain containing

Basic information

Region (hg38): 8:58552923-58582859

Links

ENSG00000137575NCBI:6386OMIM:602217HGNC:10662Uniprot:O00560AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (4 variants)

Variants pathogenicity by type

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

Variants in SDCBP

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

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

Position Type Phenotype Significance ClinVar
8-58570962-G-A Inborn genetic diseases Likely benign (Mar 27, 2023)2522334
8-58572283-T-G Inborn genetic diseases Uncertain significance (Jul 05, 2022)2215297
8-58575945-G-T Inborn genetic diseases Uncertain significance (Aug 13, 2021)2244555
8-58578055-A-G Inborn genetic diseases Uncertain significance (Mar 20, 2023)2526630

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDCBPprotein_codingprotein_codingENST00000260130 829937
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0005810.9071257140311257450.000123
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.041281660.7720.000008551962
Missense in Polyphen2038.9620.51332514
Synonymous0.02595353.20.9950.00000268580
Loss of Function1.49712.80.5495.35e-7172

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004680.000464
Ashkenazi Jewish0.0002470.000198
East Asian0.00005930.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.0001200.000114
Middle Eastern0.00005930.0000544
South Asian0.0001060.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Multifunctional adapter protein involved in diverse array of functions including trafficking of transmembrane proteins, neuro and immunomodulation, exosome biogenesis, and tumorigenesis (PubMed:26291527). Positively regulates TGFB1- mediated SMAD2/3 activation and TGFB1-induced epithelial-to- mesenchymal transition (EMT) and cell migration in various cell types. May increase TGFB1 signaling by enhancing cell-surface expression of TGFR1 by preventing the interaction between TGFR1 and CAV1 and subsequent CAV1-dependent internalization and degradation of TGFR1 (PubMed:25893292). In concert with SDC1/4 and PDCD6IP, regulates exosome biogenesis (PubMed:22660413). Regulates migration, growth, proliferation, and cell cycle progression in a variety of cancer types (PubMed:26539120). In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA) (PubMed:11498591). May also play a role in vesicular trafficking (PubMed:11179419). Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway (PubMed:10230395). {ECO:0000269|PubMed:10230395, ECO:0000269|PubMed:11179419, ECO:0000269|PubMed:11498591, ECO:0000269|PubMed:22660413, ECO:0000269|PubMed:25893292, ECO:0000269|PubMed:26539120, ECO:0000303|PubMed:26291527}.;
Pathway
miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Ectoderm Differentiation;Developmental Biology;Neutrophil degranulation;EPH-Ephrin signaling;TCR;Innate Immune System;Immune System;Ephrin signaling;IL5-mediated signaling events;Neurofascin interactions;EGFR1;L1CAM interactions;Axon guidance;IL5;Syndecan-1-mediated signaling events;Syndecan-4-mediated signaling events;Syndecan-2-mediated signaling events (Consensus)

Recessive Scores

pRec
0.364

Intolerance Scores

loftool
0.936
rvis_EVS
-0.52
rvis_percentile_EVS
21.2

Haploinsufficiency Scores

pHI
0.133
hipred
Y
hipred_score
0.626
ghis
0.610

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.903

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sdcbp
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process
negative regulation of receptor internalization;protein targeting to membrane;substrate-dependent cell migration, cell extension;chemical synaptic transmission;regulation of mitotic cell cycle;positive regulation of cell population proliferation;positive regulation of epithelial to mesenchymal transition;positive regulation of pathway-restricted SMAD protein phosphorylation;actin cytoskeleton organization;positive regulation of cell growth;positive regulation of cell migration;positive regulation of transforming growth factor beta receptor signaling pathway;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;intracellular signal transduction;positive regulation of phosphorylation;neutrophil degranulation;positive regulation of JNK cascade;ephrin receptor signaling pathway;positive regulation of exosomal secretion;positive regulation of extracellular exosome assembly
Cellular component
extracellular region;extracellular space;nucleus;nucleoplasm;cytoplasm;endoplasmic reticulum membrane;cytosol;cytoskeleton;plasma membrane;interleukin-5 receptor complex;adherens junction;focal adhesion;membrane;nuclear membrane;azurophil granule lumen;melanosome;intracellular membrane-bounded organelle;membrane raft;extracellular exosome;blood microparticle;extracellular vesicle
Molecular function
frizzled binding;interleukin-5 receptor binding;protein binding;phosphatidylinositol-4,5-bisphosphate binding;cytoskeletal adaptor activity;identical protein binding;syndecan binding;protein heterodimerization activity;protein N-terminus binding