SPRY1

sprouty RTK signaling antagonist 1

Basic information

Region (hg38): 4:123396795-123403760

Links

ENSG00000164056 ∙ NCBI:10252 ∙ OMIM:602465 ∙ HGNC:11269 ∙ Uniprot:O43609 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 23.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001258038.2	NP_001244967.1	1	yes	-
ENST00000651917.1	ENSP00000498292.1	1	yes	-
NM_005841.3	NP_005832.1	1	-	-
NM_199327.3	NP_955359.1	1	-	-

Phenotypes

GenCC

Source: genCC

• craniosynostosis (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPRY1 gene.

• not_specified (55 variants)
• SPRY1-related_disorder (5 variants)
• Inborn_genetic_diseases (1 variants)

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. These statistics are base on transcript: NM_001258038.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			55	2		57
nonsense						0
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)			1			1
Total	0	1	56	4	1

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
		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

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

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