SPRY3

protein-coding

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

Gene summary

Predicted to enable protein kinase inhibitor activity. Involved in negative regulation of MAPK cascade. Predicted to be located in cytoplasm and membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001304990.2

Inheritance

—

ClinVar variants

B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chrX:155,612,572-155,782,459

External References & Databases

Ensembl (ENSG00000168939)

Transcript & Mutation Effects

hg38 • Region Span ~169.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPRY3 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	0	1	1

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001304990.2	RefSeq	NP_001291919.1	1	MANE Select
ENST00000695325.1	Ensembl	ENSP00000511806.1	1	MANE Select
NM_001394353.1	RefSeq	NP_001381282.1	2	Standard
NM_001394354.1	RefSeq	NP_001381283.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

sprouty regulation of tyrosine kinase signals
EGFR1

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

Molecular Function

molecular_function

Cellular Component

cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302805
Coding exons: 1
Length: 14648
Individuals with no LoFs: 125572
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125591
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0198	157	158	0.996	0.00000947	1877
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00036	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as an antagonist of fibroblast growth factor (FGF) pathways and may negatively modulate respiratory organogenesis.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.552
RVIS EVS: -0.27
RVIS percentile EVS: 34.32

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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