SPOCK3

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

Basic information

Region (hg38): 4:166733383-167234796

Links

ENSG00000196104 ∙ NCBI:50859 ∙ OMIM:607989 ∙ HGNC:13565 ∙ Uniprot:Q9BQ16 ∙ 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 SPOCK3 gene.

• Inborn genetic diseases (13 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.

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	2
missense			13		2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	3

Variants in SPOCK3

This is a list of pathogenic ClinVar variants found in the SPOCK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-166734925-A-T			Benign (Jun 18, 2018)
4-166734937-T-C		not specified	Uncertain significance (Nov 17, 2023)
4-166734943-T-C		not specified	Uncertain significance (Oct 27, 2022)
4-166734966-T-G		not specified	Uncertain significance (Mar 21, 2023)
4-166735009-A-G		not specified	Uncertain significance (Dec 07, 2021)
4-166735014-G-T		not specified	Uncertain significance (Nov 09, 2023)
4-166735071-G-A			Likely benign (Jul 16, 2018)
4-166735075-A-T		not specified	Uncertain significance (Aug 22, 2023)
4-166737475-G-A		not specified	Uncertain significance (Mar 29, 2023)
4-166737503-C-T		not specified	Uncertain significance (Oct 16, 2023)
4-166737550-T-C		not specified	Uncertain significance (Dec 11, 2023)
4-166742020-C-T		not specified	Uncertain significance (Aug 22, 2023)
4-166742058-G-T		not specified	Uncertain significance (Jun 02, 2023)
4-166754657-T-C		not specified	Uncertain significance (Jan 03, 2024)
4-166792232-G-T		not specified	Uncertain significance (Jan 24, 2024)
4-166792241-C-G		not specified	Uncertain significance (Oct 03, 2022)
4-166792247-C-T		not specified	Uncertain significance (Feb 21, 2024)
4-166912700-T-C		not specified	Uncertain significance (Aug 02, 2022)
4-167000365-G-A		Inborn genetic diseases	Uncertain significance (Jan 05, 2022)
4-167000374-T-C			Benign (Jun 18, 2018)
4-167000400-G-A		not specified	Uncertain significance (Oct 29, 2021)
4-167000408-T-C			Benign (Mar 30, 2018)
4-167062518-C-A		not specified	Uncertain significance (Oct 05, 2021)
4-167062524-C-T		not specified	Uncertain significance (Feb 26, 2024)
4-167234014-C-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPOCK3	protein_coding	protein_coding	ENST00000357154	11	501413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0136	0.986	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.390	219	236	0.929	0.0000111	2914
Missense in Polyphen		72	78.665	0.91527		985
Synonymous	-1.65	104	84.7	1.23	0.00000414	739
Loss of Function	3.20	8	25.4	0.315	0.00000109	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000354	0.0000354
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000979	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

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

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

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