SPRY1

sprouty RTK signaling antagonist 1

Basic information

Region (hg38): 4:123396794-123403760

Links

ENSG00000164056 ∙ NCBI:10252 ∙ OMIM:602465 ∙ HGNC:11269 ∙ Uniprot:O43609 ∙ 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 SPRY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRY1 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				2	1	3
missense			26	2		28
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					5	5
Total	0	1	26	4	6

Variants in SPRY1

This is a list of pathogenic ClinVar variants found in the SPRY1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-123397832-T-TA		not specified	Benign (Jan 02, 2020)
4-123401439-G-A			Benign (Feb 19, 2021)
4-123401478-C-A			Benign (Jul 30, 2019)
4-123401609-A-G		SPRY1-related disorder	Likely benign (Feb 26, 2020)
4-123401611-A-G		not specified	Uncertain significance (Apr 12, 2022)
4-123401677-A-G		SPRY1-related disorder	Likely benign (Apr 08, 2019)
4-123401700-G-A		SPRY1-related disorder	Likely benign (Mar 01, 2019)
4-123401726-G-C		not specified	Uncertain significance (Apr 01, 2024)
4-123401734-G-A		not specified	Uncertain significance (Oct 20, 2021)
4-123401741-C-G		not specified	Uncertain significance (Mar 01, 2024)
4-123401745-G-C		not specified	Uncertain significance (Mar 28, 2024)
4-123401764-C-G		not specified	Uncertain significance (Oct 12, 2022)
4-123401764-C-CAG		Inborn genetic diseases	Likely pathogenic (Feb 14, 2018)
4-123401788-G-A		not specified	Uncertain significance (May 03, 2023)
4-123401788-G-T		not specified	Uncertain significance (Nov 27, 2023)
4-123401796-C-T		not specified	Uncertain significance (Dec 27, 2023)
4-123401797-C-T		not specified	Uncertain significance (Feb 22, 2023)
4-123401817-A-G		not specified	Uncertain significance (Dec 14, 2022)
4-123401833-T-C		not specified	Uncertain significance (May 04, 2022)
4-123401846-G-A		SPRY1-related disorder	Benign (Feb 10, 2020)
4-123401857-A-G		not specified	Uncertain significance (Oct 14, 2023)
4-123402019-G-C		not specified	Uncertain significance (Jun 07, 2023)
4-123402054-C-T		not specified	Uncertain significance (Jan 19, 2024)
4-123402086-C-T		SPRY1-related disorder	Likely benign (Jul 23, 2019)
4-123402121-A-C		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRY1	protein_coding	protein_coding	ENST00000394339	1	6961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00304	0.829	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.950	200	166	1.21	0.00000879	2081
Missense in Polyphen		60	58.901	1.0187		768
Synonymous	-0.719	71	63.7	1.11	0.00000340	626
Loss of Function	1.14	5	8.60	0.581	3.82e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an antagonist of fibroblast growth factor (FGF) pathways and may negatively modulate respiratory organogenesis.
• Pathway: Androgen Receptor Network in Prostate Cancer;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Signal Transduction;sprouty regulation of tyrosine kinase signals;FGF;EGFR downregulation;Signaling by EGFR;EGFR1;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.587
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.951
• hipred: Y
• hipred_score: 0.728
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.774

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spry1
• Phenotype: endocrine/exocrine gland phenotype; renal/urinary system phenotype; neoplasm; 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); normal phenotype

Gene ontology

• Biological process: establishment of mitotic spindle orientation;metanephros development;ureteric bud development;organ induction;negative regulation of cell population proliferation;negative regulation of GTPase activity;negative regulation of fibroblast growth factor receptor signaling pathway;negative regulation of epidermal growth factor receptor signaling pathway;negative regulation of MAP kinase activity;negative regulation of Ras protein signal transduction;negative regulation of neurotrophin TRK receptor signaling pathway;bud elongation involved in lung branching;epithelial to mesenchymal transition involved in cardiac fibroblast development;negative regulation of ERK1 and ERK2 cascade
• Cellular component: nucleoplasm;Golgi apparatus;cytosol;plasma membrane
• Molecular function: protein binding