SPOCK2
Basic information
Region (hg38): 10:72059034-72089032
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 3 | |||||
missense | 39 | 43 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 39 | 3 | 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) | ||
10-72062836-G-A | not specified | Uncertain significance (Oct 19, 2024) | ||
10-72062851-T-C | not specified | Uncertain significance (Mar 01, 2024) | ||
10-72062882-C-T | not specified | Uncertain significance (Feb 22, 2025) | ||
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) | ||
10-72063048-C-T | not specified | Uncertain significance (Jul 30, 2024) | ||
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) | ||
10-72064207-T-C | not specified | Uncertain significance (Jun 05, 2024) | ||
10-72064211-T-C | not specified | Likely benign (Aug 15, 2024) | ||
10-72064214-G-A | not specified | Uncertain significance (Oct 20, 2023) | ||
10-72067012-A-G | not specified | Uncertain significance (Feb 21, 2025) | ||
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) |
GnomAD
Source:
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:
- 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
- essential_gene_gene_trap
- 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
- Phenotype
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