SPRY3

sprouty RTK signaling antagonist 3, the group of Pseudoautosomal region 2

Basic information

Region (hg38): X:155612572-155782459

Links

ENSG00000168939

∙ NCBI:10251 ∙ OMIM:300531 ∙ HGNC:11271 ∙ Uniprot:O43610 ∙ 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 SPRY3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRY3 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					1 clinvar	1
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	1

Variants in SPRY3

This is a list of pathogenic ClinVar variants found in the SPRY3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-155773926-C-T		Ependymoma	Uncertain significance (Dec 29, 2017)	487791
X-155773979-A-G			Benign (Apr 16, 2018)	726033

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRY3	protein_coding	protein_coding	ENST00000302805	1	14648

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00381	0.862	125572	0	19	125591	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0198	157	158	0.996	0.00000947	1877
Missense in Polyphen		46	48.686	0.94483		586
Synonymous	-0.306	63	60.0	1.05	0.00000305	597
Loss of Function	1.26	5	9.10	0.550	5.74e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000617	0.0000617
Middle Eastern	0.0000544	0.0000544
South Asian	0.000359	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May function as an antagonist of fibroblast growth factor (FGF) pathways and may negatively modulate respiratory organogenesis.;
Pathway: sprouty regulation of tyrosine kinase signals;EGFR1 (Consensus)

Recessive Scores

pRec: 0.115

Intolerance Scores

loftool: 0.552
rvis_EVS: -0.27
rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

pHI: 0.652
hipred: N
hipred_score: 0.248
ghis: 0.580

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Spry3
Phenotype

Gene ontology

Biological process: multicellular organism development;negative regulation of fibroblast growth factor receptor signaling pathway;negative regulation of MAP kinase activity;negative regulation of Ras protein signal transduction;axon development
Cellular component: cytosol;membrane
Molecular function: molecular_function