SPOCK3

SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3, the group of SPARC family

Basic information

Region (hg38): 4:166733384-167234796

Links

ENSG00000196104NCBI:50859OMIM:607989HGNC:13565Uniprot:Q9BQ16AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPOCK3 gene.

  • not_specified (49 variants)
  • not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPOCK3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040159.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
3
missense
48
clinvar
2
clinvar
50
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 48 2 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SPOCK3protein_codingprotein_codingENST00000357154 11501413
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01360.9861257340141257480.0000557
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3902192360.9290.00001112914
Missense in Polyphen7278.6650.91527985
Synonymous-1.6510484.71.230.00000414739
Loss of Function3.20825.40.3150.00000109305

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003540.0000354
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004630.0000462
European (Non-Finnish)0.00009790.0000967
Middle Eastern0.000.00
South Asian0.00003280.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May participate in diverse steps of neurogenesis. Inhibits the processing of pro-matrix metalloproteinase 2 (MMP-2) by MT1-MMP and MT3-MMP. May interfere with tumor invasion.;
Pathway
Extracellular matrix organization;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix (Consensus)

Recessive Scores

pRec
0.119

Intolerance Scores

loftool
0.623
rvis_EVS
0.04
rvis_percentile_EVS
57.31

Haploinsufficiency Scores

pHI
0.127
hipred
Y
hipred_score
0.543
ghis
0.514

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.687

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Spock3
Phenotype
normal phenotype;

Gene ontology

Biological process
negative regulation of endopeptidase activity;peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan;negative regulation of cell motility
Cellular component
extracellular space
Molecular function
calcium ion binding;collagen binding;glycosaminoglycan binding;metalloendopeptidase inhibitor activity;extracellular matrix binding