SDC3

protein-coding

syndecan 3, the group of Syndecans

Gene summary

The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]

MANE transcript

NM_014654.4

Inheritance

—

ClinVar variants

U:79B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr1:30,869,466-30,908,758

External References & Databases

Ensembl (ENSG00000162512)

Transcript & Mutation Effects

hg38 • Region Span ~39.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SDC3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014654.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	1 clinvar	4
missense			75 clinvar	4 clinvar	2 clinvar	81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	79	5	3	87

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014654.4	RefSeq	NP_055469.3	5	MANE Select
ENST00000339394.7	Ensembl	ENSP00000344468.6	5	MANE Select
ENST00000336798.11	Ensembl	ENSP00000338346.7	3	Standard
ENST00000336798.12	Ensembl	ENSP00000338346.7	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
sdc3	Danio rerio	Structure: pronephric glomerulus Quality: lacks parts or has fewer parts of type abnormal

Gene / Model

Organism

Observed Phenotype

sdc3

Danio rerio

Structure: pronephric glomerulus

Quality: lacks parts or has fewer parts of type

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell adhesion molecules (CAMs) - Homo sapiens (human)
Signaling by GPCR
Signal Transduction
Metabolism of fat-soluble vitamins
Metabolism of carbohydrates

Biological Process

retinoid metabolic process
glycosaminoglycan biosynthetic process
glycosaminoglycan catabolic process
cell migration
leukocyte migration

Molecular Function

protein binding
identical protein binding

Cellular Component

Golgi lumen
plasma membrane
cell surface
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339394
Coding exons: 5
Length: 39295
Individuals with no LoFs: 125741
Homozygous LoFs: 1
Heterozygous LoFs: 4
Defined: 125746
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.179	246	254	0.968	0.0000157	2757
Missense (PolyPhen)		53	55.048	0.96279		537
Synonymous	-1.31	133	115	1.16	0.00000780	1063
Loss of Function	2.25	2	9.48	0.211	4.00e-7	126

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000010	0.0000088	rare
South Asian	0.00011	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cell surface proteoglycan that may bear heparan sulfate (By similarity). May have a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. {ECO:0000250, ECO:0000269|PubMed:11527150}.;

Recessive Scores

pRec: 0.318

Intolerance Scores

LoFtool: 0.216
RVIS EVS: -0.02
RVIS percentile EVS: 52.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.652

Gene Damage Prediction

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