SPRY2
sprouty RTK signaling antagonist 2
Basic information
Region (hg38): 13:80335976-80341126
Links
Phenotypes
GenCC
Source:
- Tourette syndrome (Limited), mode of inheritance: Unknown
- IgA nephropathy, susceptibility to, 3 (Limited), mode of inheritance: AD
- IgA nephropathy, susceptibility to, 3 (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| IgA nephropathy, susceptibility to, 3 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Renal | 25782674 |
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 SPRY2 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 | 0 | |||||
| missense | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 20 | 0 | 1 |
Variants in SPRY2
This is a list of pathogenic ClinVar variants found in the SPRY2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-80336651-C-A | Benign (May 26, 2021) | |||
| 13-80336762-G-A | IgA nephropathy, susceptibility to, 3 | Uncertain significance (Jan 04, 2021) | ||
| 13-80336786-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 13-80336811-CTG-C | SPRY2-related disorder | Uncertain significance (Feb 15, 2023) | ||
| 13-80336836-A-G | SPRY2-related disorder | Likely benign (Jan 31, 2023) | ||
| 13-80336864-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
| 13-80337090-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
| 13-80337194-A-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 13-80337200-T-A | not specified | Uncertain significance (May 04, 2022) | ||
| 13-80337251-A-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 13-80337254-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 13-80337255-G-A | not specified | Uncertain significance (Dec 07, 2024) | ||
| 13-80337255-G-C | not specified | Uncertain significance (Dec 15, 2023) | ||
| 13-80337279-C-G | not specified | Uncertain significance (Apr 01, 2024) | ||
| 13-80337280-G-A | SPRY2-related disorder | Benign (Oct 28, 2019) | ||
| 13-80337296-C-G | IgA nephropathy, susceptibility to, 3 | Uncertain significance (Oct 25, 2019) | ||
| 13-80337336-T-C | not specified | Uncertain significance (Jun 04, 2024) | ||
| 13-80337344-C-G | SPRY2-related disorder | Uncertain significance (Aug 21, 2024) | ||
| 13-80337351-G-A | IgA nephropathy, susceptibility to, 3 | risk factor (Sep 18, 2019) | ||
| 13-80337377-G-C | not specified | Uncertain significance (Sep 14, 2022) | ||
| 13-80337432-G-A | not specified | Uncertain significance (Sep 26, 2023) | ||
| 13-80337571-C-A | not specified | Uncertain significance (May 27, 2022) | ||
| 13-80337596-T-G | not specified | Uncertain significance (Jun 18, 2021) | ||
| 13-80337632-C-T | not specified | Uncertain significance (Jan 06, 2023) | ||
| 13-80337687-T-C | not specified | Uncertain significance (Jul 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SPRY2 | protein_coding | protein_coding | ENST00000377102 | 1 | 4976 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.971 | 0.0287 | 125711 | 0 | 1 | 125712 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.974 | 139 | 175 | 0.793 | 0.0000101 | 2039 |
| Missense in Polyphen | 42 | 69.913 | 0.60075 | 897 | ||
| Synonymous | -1.37 | 87 | 72.2 | 1.21 | 0.00000443 | 649 |
| Loss of Function | 3.07 | 0 | 11.0 | 0.00 | 7.20e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May function as an antagonist of fibroblast growth factor (FGF) pathways and may negatively modulate respiratory organogenesis. {ECO:0000269|PubMed:10887178}.;
- Disease
- DISEASE: IgA nephropathy 3 (IGAN3) [MIM:616818]: A form of IgA nephropathy, a common primary glomerulonephritis characterized by glomerular sclerosis, interstitial fibrosis, and mesangial glomerular deposits of immunoglobulin A and immunoglobulin G visible on renal biopsies. IgA nephropathy is associated with renal insufficiency that can progress to end-stage renal disease. Proteinuria and hematuria are characteristic clinical presentations. {ECO:0000269|PubMed:25782674}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- MicroRNAs in cancer - Homo sapiens (human);Signaling Pathways in Glioblastoma;Androgen Receptor Network in Prostate Cancer;Ectoderm Differentiation;EGF-EGFR Signaling Pathway;Negative regulation of FGFR2 signaling;Signaling by FGFR2;Negative regulation of FGFR3 signaling;Signaling by FGFR3;Signal Transduction;Negative regulation of FGFR4 signaling;Signaling by FGFR4;Signaling by FGFR;Spry regulation of FGF signaling;sprouty regulation of tyrosine kinase signals;EGFR downregulation;Signaling by EGFR;EGFR1;Signaling by Receptor Tyrosine Kinases;Internalization of ErbB1;Signaling events mediated by PTP1B;FGF signaling pathway;Negative regulation of FGFR1 signaling;Signaling by FGFR1
(Consensus)
Intolerance Scores
- loftool
- 0.0887
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.722
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.494
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Spry2
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; skeleton phenotype; respiratory system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype;
Zebrafish Information Network
- Gene name
- spry2
- Affected structure
- neural plate
- Phenotype tag
- abnormal
- Phenotype quality
- increased width
Gene ontology
- Biological process
- establishment of mitotic spindle orientation;sensory perception of sound;negative regulation of cell population proliferation;positive regulation of gene expression;negative regulation of peptidyl-threonine phosphorylation;negative regulation of angiogenesis;positive regulation of cell migration;negative regulation of cell projection organization;positive regulation of peptidyl-serine phosphorylation;negative regulation of GTPase activity;cellular response to vascular endothelial growth factor stimulus;negative regulation of fibroblast growth factor receptor signaling pathway;negative regulation of epidermal growth factor receptor signaling pathway;inner ear morphogenesis;negative regulation of apoptotic process;negative regulation of MAP kinase activity;cell fate commitment;regulation of cell differentiation;negative regulation of Ras protein signal transduction;negative regulation of neurotrophin TRK receptor signaling pathway;positive regulation of protein kinase B signaling;lung growth;bud elongation involved in lung branching;negative regulation of ERK1 and ERK2 cascade;positive regulation of ERK1 and ERK2 cascade;positive regulation of protein serine/threonine kinase activity;negative regulation of vascular endothelial growth factor signaling pathway;cellular response to leukemia inhibitory factor
- Cellular component
- nucleus;cytosol;cytoskeleton;microtubule;plasma membrane;microtubule cytoskeleton;membrane;ruffle membrane
- Molecular function
- protein binding;protein kinase binding;protein serine/threonine kinase inhibitor activity;protein serine/threonine kinase activator activity