SPOCK2

protein-coding

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

Gene summary

This gene encodes a protein which binds with glycosaminoglycans to form part of the extracellular matrix. The protein contains thyroglobulin type-1, follistatin-like, and calcium-binding domains, and has glycosaminoglycan attachment sites in the acidic C-terminal region. Three alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_001244950.2

Inheritance

—

ClinVar variants

U:62B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr10:72,059,034-72,089,032

External References & Databases

Ensembl (ENSG00000107742)

Transcript & Mutation Effects

hg38 • Region Span ~30.0 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 SPOCK2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001244950.2. 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				1 clinvar	2 clinvar	3
missense			61 clinvar	2 clinvar	2 clinvar	65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	62	3	4	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001244950.2	RefSeq	NP_001231879.1	11	MANE Select
ENST00000373109.7	Ensembl	ENSP00000362201.2	11	MANE Select
NM_001134434.1	RefSeq	NP_001127906.1	2	Standard
NM_014767.2	RefSeq	NP_055582.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

calcium ion binding
collagen binding
glycosaminoglycan binding
metalloendopeptidase inhibitor activity
extracellular matrix binding

Cellular Component

extracellular space
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373109
Coding exons: 11
Length: 29998
Individuals with no LoFs: 125700
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125708
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.13	199	249	0.799	0.0000146	2758
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000071	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.664

Gene Damage Prediction

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