SPOCK1

protein-coding

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

Gene summary

This gene encodes the protein core of a seminal plasma proteoglycan containing chondroitin- and heparan-sulfate chains. The protein's function is unknown, although similarity to thyropin-type cysteine protease-inhibitors suggests its function may be related to protease inhibition. [provided by RefSeq, Jul 2008]

Previous symbols:

TIC1
SPOCK

MANE transcript

NM_004598.4

Inheritance

—

ClinVar variants

U:53B:6

Top phenotype

SPOCK1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr5:136,975,298-137,598,379

External References & Databases

Ensembl (ENSG00000152377)

Transcript & Mutation Effects

hg38 • Region Span ~623.1 kb

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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 SPOCK1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 48

SPOCK1-related disorderTotal: 3

not providedTotal: 2

MicrocephalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004598.4. 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	3 clinvar		5
missense			50 clinvar	2 clinvar	1 clinvar	53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	53	5	1	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004598.4	RefSeq	NP_004589.1	10	MANE Select
ENST00000394945.6	Ensembl	ENSP00000378401.1	10	MANE Select
ENST00000505690.1	Ensembl	ENSP00000424517.1	4	Standard
ENST00000510689.5	Ensembl	ENSP00000421677.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Adipogenesis

Biological Process

regulation of cell growth
neuron migration
cell adhesion
nervous system development
negative regulation of cell-substrate adhesion

Molecular Function

serine-type endopeptidase inhibitor activity
cysteine-type endopeptidase inhibitor activity
calcium ion binding
collagen binding
metalloendopeptidase inhibitor activity

Cellular Component

extracellular space
cytoplasm
postsynaptic density
sarcoplasm
neuromuscular junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394945
Coding exons: 10
Length: 623082
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125746
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.18	190	242	0.786	0.0000124	2886
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.206

Intolerance Scores

LoFtool: 0.542
RVIS EVS: -0.49
RVIS percentile EVS: 22.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0552

Gene Damage Prediction

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