SPRY4-IT1

Chr 5AD

SPRY4 intronic transcript 1

Also known as: SPRIGHTLY

NCBI Gene: 100642175

This gene produces a non-coding RNA that is upregulated in several different tumors, including melanoma and breast and prostate cancer cells. This transcript may mediate cell growth, proliferation, and apoptosis. It regulates levels of lipin 2, and therefore may be involved in lipid biosynthesis. The primary transcript is cleaved to release a mature product that localizes to the cytoplasm (PMID:25344859). The full length structure of the primary and cleaved transcripts is unclear, and it is possible that the primary transcript is a splice variant of SPRY4 (sprouty RTK signaling antagonist 4). [provided by RefSeq, Feb 2016]

Primary Disease Associations & Inheritance

Hypogonadotropic hypogonadism 17 with or without anosmiaMIM #615266
AD
0
Active trials
5
Pathogenic / LP
6
ClinVar variants
2
Pubs (1 yr)
—
Missense Z
—
LOEUF
Clinical Summary— SPRY4-IT1
📋
ClinVar Variants
5 Pathogenic / Likely Pathogenic· 1 VUS of 6 total submissions
Some data sources returned errors (3)

ensembl: Error: Ensembl fetch failed: 400 for https://rest.ensembl.org/lookup/symbol/homo_sapiens/SPRY4-IT1?content-type=application/json&expand=1

gnomad: Error: Gene not found

pubtator: TimeoutError: The operation was aborted due to timeout

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

ClinVar Variant Classifications

6 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5
VUS1
5
Pathogenic
1
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
————5
Likely Pathogenic
————0
VUS
————1
Likely Benign
————0
Benign
————0
Total—6

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

SPRY4-IT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Dissecting the role of SPRY4-IT1 and TUG1 in modulating miR-425/TGF-β/ Smad signaling in mediating renal fibrosis and inflammation in lupus nephritis: Novel biomarkers and therapeutic targets.
Abd-Elmawla MA et al.·Int Immunopharmacol
2025
Retraction Notice to: lncRNA SPRY4-IT1 Regulates Cell Proliferation and Migration by Sponging miR-101-3p and Regulating AMPK Expression in Gastric Cancer.
Cao S et al.·Mol Ther Nucleic Acids
2024Open Access
LncRNA SPRY4-IT1 regulates 16HBE cell malignant transformation induced by particulate matter through DUSP6-ERK1/2-Chk1 signaling pathway.
Li Y et al.·Chemosphere
2023
PDK1-stabilized LncRNA SPRY4-IT1 promotes breast cancer progression via activating NF-κB signaling pathway.
Zhang Y et al.·Mol Carcinog
2023
LncRNA SPRY4‑IT1 is upregulated and promotes the proliferation of prostate cancer cells under hypoxia in vitro.
Sang W et al.·Oncol Lett
2023Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients