HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SIPA1L3
signal induced proliferation associated 1 like 3
Chromosome 19 Β· 19q13.13-q13.2
NCBI Gene: 23094Ensembl: ENSG00000105738.12HGNC: HGNC:23801UniProt: B2RWP0
72PubMed Papers
21Diseases
0Drugs
2Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
stress fiberepithelial cell morphogenesisapical part of celltricellular tight junctionearly-onset non-syndromic cataractTotal congenital cataracttotal early-onset cataracthyperuricemia
✦AI Summary

SIPA1L3 (signal-induced proliferation-associated 1 like 3) is a GTPase-activating protein (GAP) that plays a critical role in epithelial cell morphogenesis, polarity, adhesion, and cytoskeletal organization, particularly in the lens 1. The protein regulates Rap family GTPases through its Rap-GAP domain and is essential for proper eye and lens development 2. SIPA1L3 functions within an Epha4/Sipa1l3/Wnt signaling pathway that controls eye specification and lens fiber cell maturation; loss of either Epha4 or Sipa1l3 results in smaller eyes and lenses due to dysregulated canonical Wnt signaling 3. In neuronal tissue, SIPA1L3/SPAR3 localizes to excitatory postsynapses and interacts with postsynaptic scaffold proteins, suggesting a role in synaptic function 4. Mutations in SIPA1L3 cause autosomal recessive congenital cataracts 2, representing one of the most important causes of blindness in infancy. Pathogenic variants disrupt epithelial cell organization, cell polarity, and adherens junction formation, leading to abnormal epithelial-to-mesenchymal transition in the lens 1. Additionally, SIPA1L3 variants have been identified in association with kidney disease susceptibility 5, suggesting broader physiological roles beyond ocular development.

Sources cited
1
SIPA1L3 identified as novel gene for autosomal recessive congenital cataract via homozygous nonsense variant; encodes Rap GTPase-activating protein crucial for lens development
PMID: 25804400
2
SIPA1L3 interacts directly with Epha4 in Epha4/Sipa1l3/Wnt pathway regulating eye development and lens fiber cell maturation; loss causes smaller eyes/lenses through dysregulated Wnt signaling
PMID: 27993984
3
SIPA1L3 mutations cause lens and eye abnormalities through disruption of epithelial cell morphogenesis, polarity, adhesion, cytoskeletal organization, and epithelial-to-mesenchymal transition
PMID: 26231217
4
Sipa1l3/SPAR3 is targeted to excitatory postsynapses and interacts with postsynaptic Fezzin proteins, functioning as synaptic RapGAP
PMID: 26364583
5
SIPA1L3 variants identified as contribution to chronic kidney disease and end-stage kidney disease susceptibility through both common and rare variants
PMID: 40770708
Disease Associationsβ“˜21
early-onset non-syndromic cataractOpen Targets
0.56Moderate
Total congenital cataractOpen Targets
0.39Weak
total early-onset cataractOpen Targets
0.37Weak
hyperuricemiaOpen Targets
0.33Weak
prostate carcinomaOpen Targets
0.28Weak
myeloproliferative disorderOpen Targets
0.28Weak
nephrotic syndromeOpen Targets
0.25Weak
chronic kidney diseaseOpen Targets
0.25Weak
cutaneous melanomaOpen Targets
0.23Weak
poisoningOpen Targets
0.23Weak
response to antibioticOpen Targets
0.23Weak
brain compressionOpen Targets
0.22Weak
edemaOpen Targets
0.22Weak
smoking initiationOpen Targets
0.20Weak
cervical carcinomaOpen Targets
0.17Weak
alcohol drinkingOpen Targets
0.16Weak
hearing lossOpen Targets
0.14Weak
Sensorineural hearing impairmentOpen Targets
0.11Weak
Abnormality of the skeletal systemOpen Targets
0.10Weak
prostate cancerOpen Targets
0.09Suggestive
Cataract 45UniProt
Pathogenic Variants2
NM_015073.3(SIPA1L3):c.3492dup (p.Gly1165fs)Pathogenic
Cataract 45
β˜…β˜†β˜†β˜†2022β†’ Residue 1165
NM_015073.3(SIPA1L3):c.4489C>T (p.Arg1497Ter)Pathogenic
Cataract 45
β˜†β˜†β˜†β˜†2017β†’ Residue 1497
View on ClinVar β†—
Related Genes
LZTS3Protein interaction72%ARHGAP10Shared pathway33%FGD2Shared pathway22%FGD5Shared pathway22%FGD4Shared pathway22%FGD3Shared pathway22%
Tissue Expression6 tissues
Lung
100%
Brain
83%
Heart
81%
Bone Marrow
73%
Liver
73%
Ovary
65%
Gene Interaction Network
Click a node to explore
SIPA1L3LZTS3ARHGAP10FGD2FGD5FGD4FGD3
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt O60292
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.56Moderately Constrained
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.45 [0.36–0.56]
RankingsWhere SIPA1L3 stands among ~20K protein-coding genes
  • #6,586of 20,598
    Most Researched72
  • #4,377of 5,498
    Most Pathogenic Variants2
  • #3,628of 17,882
    Most Constrained (LOEUF)0.56 Β· top quartile
Genes detectedSIPA1L3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
SIPA1L3 identified by linkage analysis and whole-exome sequencing as a novel gene for autosomal recessive congenital cataract.
PMID: 25804400
Eur J Hum Genet Β· 2015
1.00
2
An Epha4/Sipa1l3/Wnt pathway regulates eye development and lens maturation.
PMID: 27993984
Development Β· 2017
0.90
3
Identification of the cytoplasmic DNA-Sensing cGAS-STING pathway-mediated gene signatures and molecular subtypes in prostate cancer.
PMID: 38877472
BMC Cancer Β· 2024
0.80
4
Longitudinal DNA methylation and cell-type proportions alterations in risperidone treatment response in first-episode psychosis.
PMID: 40393579
Prog Neuropsychopharmacol Biol Psychiatry Β· 2025
0.70
5
Sipa1l3/SPAR3 is targeted to postsynaptic specializations and interacts with the Fezzin ProSAPiP1/Lzts3.
PMID: 26364583
J Neurochem Β· 2016
0.60