SPOCK1

SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1, the group of SPARC family

Basic information

Region (hg38): 5:136975297-137598379

Previous symbols: [ "TIC1", "SPOCK" ]

Links

ENSG00000152377 ∙ NCBI:6695 ∙ OMIM:602264 ∙ HGNC:11251 ∙ Uniprot:Q08629 ∙ 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 SPOCK1 gene.

• Inborn genetic diseases (23 variants)
• not specified (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPOCK1 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
missense			22	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	1

Variants in SPOCK1

This is a list of pathogenic ClinVar variants found in the SPOCK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-136978733-C-G		not specified	Uncertain significance (Nov 08, 2022)
5-136988483-G-C		not specified	Uncertain significance (Apr 13, 2022)
5-136988503-G-T		not specified	Uncertain significance (Dec 20, 2023)
5-136988518-C-T		not specified	Uncertain significance (May 17, 2023)
5-136988534-G-T		SPOCK1-related disorder	Likely benign (Aug 14, 2019)
5-136988566-G-C		not specified	Uncertain significance (Mar 22, 2023)
5-136988596-T-C		not specified	Uncertain significance (Feb 10, 2022)
5-136988629-T-C		not specified	Uncertain significance (Jul 11, 2023)
5-136992523-T-C		not specified	Uncertain significance (Dec 27, 2023)
5-136992552-C-A		not specified	Uncertain significance (Mar 22, 2023)
5-136992580-G-A		not specified	Uncertain significance (Jun 22, 2023)
5-137067739-G-C		not specified	Uncertain significance (Sep 28, 2022)
5-137067781-G-T		not specified	Uncertain significance (Aug 13, 2021)
5-137067787-C-T		not specified	Likely benign (Apr 08, 2022)
5-137067796-T-C		not specified	Uncertain significance (Jun 22, 2023)
5-137067817-A-G		not specified	Uncertain significance (May 27, 2022)
5-137112481-T-C		not specified	Uncertain significance (Jan 16, 2024)
5-137112488-C-T		not specified	Uncertain significance (Jun 30, 2023)
5-137112490-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-137112496-G-T		not specified	Uncertain significance (Feb 28, 2023)
5-137112511-A-C		not specified	Uncertain significance (Mar 22, 2023)
5-137112516-C-T		SPOCK1-related disorder	Likely benign (Feb 28, 2019)
5-137112517-G-A		not specified	Uncertain significance (Apr 13, 2022)
5-137112517-G-C		not specified	Uncertain significance (Apr 11, 2023)
5-137140599-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPOCK1	protein_coding	protein_coding	ENST00000394945	10	623082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.826	0.174	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	190	242	0.786	0.0000124	2886
Missense in Polyphen		71	103.28	0.68747		1268
Synonymous	-0.0533	103	102	1.01	0.00000579	790
Loss of Function	3.71	4	23.4	0.171	0.00000108	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cell-cell and cell-matrix interactions. May contribute to various neuronal mechanisms in the central nervous system.
• Pathway: Adipogenesis (Consensus)

Recessive Scores

• pRec: 0.206

Intolerance Scores

• loftool: 0.542
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.288
• hipred: Y
• hipred_score: 0.513
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0552

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spock1
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of cell growth;neuron migration;cell adhesion;nervous system development;negative regulation of cell-substrate adhesion;negative regulation of endopeptidase activity;negative regulation of neuron projection development;central nervous system neuron differentiation;neurogenesis
• Cellular component: extracellular space;cytoplasm;postsynaptic density;sarcoplasm;neuromuscular junction;node of Ranvier
• Molecular function: serine-type endopeptidase inhibitor activity;cysteine-type endopeptidase inhibitor activity;calcium ion binding;collagen binding;metalloendopeptidase inhibitor activity;extracellular matrix binding