SPOCK2

SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2, the group of SPARC family

Basic information

Region (hg38): 10:72059033-72089032

Links

ENSG00000107742 ∙ NCBI:9806 ∙ OMIM:607988 ∙ HGNC:13564 ∙ Uniprot:Q92563 ∙ 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 SPOCK2 gene.

• Inborn genetic diseases (20 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPOCK2 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	2	3
missense			19	1	2	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	4

Variants in SPOCK2

This is a list of pathogenic ClinVar variants found in the SPOCK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-72062770-T-C		not specified	Uncertain significance (Aug 17, 2022)
10-72062777-C-T		not specified	Uncertain significance (Dec 15, 2023)
10-72062811-C-G		not specified	Uncertain significance (Jan 31, 2023)
10-72062851-T-C		not specified	Uncertain significance (Mar 01, 2024)
10-72062886-C-T			Benign (Apr 16, 2018)
10-72062887-G-A		not specified	Uncertain significance (Jul 28, 2021)
10-72062897-C-T		not specified	Uncertain significance (Nov 17, 2022)
10-72063031-C-T		not specified	Uncertain significance (Jan 23, 2024)
10-72063045-G-A		not specified	Uncertain significance (Sep 21, 2023)
10-72063051-G-A		not specified	Uncertain significance (May 31, 2023)
10-72063097-C-T			Benign (Dec 31, 2019)
10-72063102-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-72063142-C-T		not specified	Uncertain significance (Jul 06, 2021)
10-72064193-C-A		not specified	Uncertain significance (Sep 29, 2023)
10-72064214-G-A		not specified	Uncertain significance (Oct 20, 2023)
10-72067016-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-72067017-G-A			Benign (Dec 31, 2019)
10-72067018-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-72067063-T-C		not specified	Uncertain significance (Oct 06, 2023)
10-72067091-T-C		not specified	Uncertain significance (Oct 06, 2021)
10-72067100-C-A		not specified	Uncertain significance (Apr 05, 2023)
10-72067621-G-A		not specified	Uncertain significance (Jan 05, 2022)
10-72067621-G-C		not specified	Uncertain significance (Jan 09, 2024)
10-72067628-C-T		not specified	Uncertain significance (Mar 20, 2023)
10-72067646-C-G		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPOCK2	protein_coding	protein_coding	ENST00000373109	11	29998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.241	0.759	125700	0	8	125708	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	199	249	0.799	0.0000146	2758
Missense in Polyphen		60	76.895	0.78029		781
Synonymous	-0.140	111	109	1.02	0.00000744	758
Loss of Function	3.52	6	24.9	0.241	0.00000116	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000133	0.000132
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in diverse steps of neurogenesis. Binds calcium.

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.184
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.08

Haploinsufficiency Scores

• pHI: 0.294
• hipred: Y
• hipred_score: 0.699
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spock2

Gene ontology

• Biological process: synapse assembly;positive regulation of cell-substrate adhesion;negative regulation of endopeptidase activity;peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan;extracellular matrix organization;regulation of cell differentiation;cellular response to leukemia inhibitory factor;positive regulation of cell motility
• Cellular component: extracellular space;extracellular matrix
• Molecular function: calcium ion binding;collagen binding;glycosaminoglycan binding;metalloendopeptidase inhibitor activity;extracellular matrix binding