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Aliases for SIPA1L3 Gene

Aliases for SIPA1L3 Gene

  • Signal Induced Proliferation Associated 1 Like 3 2 3 5
  • Signal-Induced Proliferation-Associated 1-Like Protein 3 3 4
  • SIPA1-Like Protein 3 3 4
  • SPA-1-Like Protein 3 3 4
  • SPAL3 3 4
  • Signal-Induced Proliferation-Associated 1 Like 3 2
  • Spine-Associated RapGAP 3 3
  • Spine‐Associated RapGAP 3 2
  • KIAA0545 4
  • CTRCT45 3
  • SPAR3 3

External Ids for SIPA1L3 Gene

Previous GeneCards Identifiers for SIPA1L3 Gene

  • GC19P043090
  • GC19P043264
  • GC19P038397
  • GC19P034846

Summaries for SIPA1L3 Gene

Entrez Gene Summary for SIPA1L3 Gene

  • This gene belongs to the signal induced proliferation associated 1 family of genes, which encode GTPase-activating proteins specific for the GTP-binding protein Rap1. Rap1 has been implicated in regulation of cell adhesion, cell polarity, and organization of the cytoskeleton. Like other members of the family, the protein encoded by this gene contains RapGAP and PDZ domains. In addition, this protein contains a C-terminal leucine zipper domain. This gene is proposed to function in epithelial cell morphogenesis and establishment or maintenance of polarity. Consistently, expression of the protein in cell culture showed localization to cell-cell borders in apical regions, and downregulation of the gene in 3D Caco2 cell culture resulted in abnormal cell polarity and morphogenesis. Allelic variants of this gene have been associated with congenital cataracts in humans. [provided by RefSeq, Feb 2016]

GeneCards Summary for SIPA1L3 Gene

SIPA1L3 (Signal Induced Proliferation Associated 1 Like 3) is a Protein Coding gene. Diseases associated with SIPA1L3 include Cataract 45 and Cataract 44. Among its related pathways are Ras signaling pathway. Gene Ontology (GO) annotations related to this gene include GTPase activator activity. An important paralog of this gene is SIPA1L1.

UniProtKB/Swiss-Prot for SIPA1L3 Gene

  • Plays a critical role in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organization in the lens (PubMed:26231217).

Additional gene information for SIPA1L3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SIPA1L3 Gene

Genomics for SIPA1L3 Gene

GeneHancer (GH) Regulatory Elements for SIPA1L3 Gene

Promoters and enhancers for SIPA1L3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J037905 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 600.7 +0.5 493 4.2 ELF3 ZKSCAN8 SIX5 ZNF148 NKRF ZNF121 ZNF384 ZNF687 ZSCAN21 BACH1 WDR87 SIPA1L3 ZFP30 ZNF527 ZNF875 ZNF383 ZNF607 ZNF571 HNRNPL LINC01535
GH19J037959 Promoter/Enhancer 1 EPDnew dbSUPER 611.5 +52.5 52512 0.1 ZBTB33 TRIM22 YBX1 HDGF NBN ATF7 TARDBP SIPA1L3 WDR87 ENSG00000268051 GC19P037934
GH19J038181 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.5 +276.3 276323 3.3 EGR1 HDAC2 ZNF623 NFIC ZFHX2 ZNF189 BCOR VEZF1 PRDM10 ZNF280D ENSG00000269653 SIPA1L3 C19orf33 ENSG00000267892 ZNF573 DPF1 ZNF607 GC19M040734
GH19J038171 Promoter/Enhancer 1.2 Ensembl ENCODE dbSUPER 24.5 +266.0 266031 2.7 MGA MNT BCOR HIC1 ADNP ZMYM3 L3MBTL2 SIPA1L3 ENSG00000269653 GC19M040734
GH19J038043 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 19.9 +139.9 139873 6.7 ZNF473 SP1 NKRF ZNF687 CTCF RELA CREM MLLT1 RAD21 ZBED1 SIPA1L3 ZNF571 ZNF585B ZNF875 ZNF527 ZNF573 WDR87 ZNF383 ENSG00000267682 ZNF607
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SIPA1L3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SIPA1L3 Gene

Genomic Locations for SIPA1L3 Gene
301,165 bases
Plus strand
301,145 bases
Plus strand

Genomic View for SIPA1L3 Gene

Genes around SIPA1L3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SIPA1L3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SIPA1L3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SIPA1L3 Gene

Proteins for SIPA1L3 Gene

  • Protein details for SIPA1L3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Signal-induced proliferation-associated 1-like protein 3
    Protein Accession:
    Secondary Accessions:
    • Q2TV87

    Protein attributes for SIPA1L3 Gene

    1781 amino acids
    Molecular mass:
    194610 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SIPA1L3 Gene

Post-translational modifications for SIPA1L3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SIPA1L3 Gene

No data available for DME Specific Peptides for SIPA1L3 Gene

Domains & Families for SIPA1L3 Gene

Gene Families for SIPA1L3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SIPA1L3 Gene

Suggested Antigen Peptide Sequences for SIPA1L3 Gene

GenScript: Design optimal peptide antigens:
  • Signal-induced proliferation-associated 1 like 3 (B2RWP0_HUMAN)
  • SIPA1L3 protein (Q8IUV1_HUMAN)
  • SPA-1-like protein 3 (SI1L3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SIPA1L3: view

No data available for UniProtKB/Swiss-Prot for SIPA1L3 Gene

Function for SIPA1L3 Gene

Molecular function for SIPA1L3 Gene

UniProtKB/Swiss-Prot Function:
Plays a critical role in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organization in the lens (PubMed:26231217).

Phenotypes From GWAS Catalog for SIPA1L3 Gene

Gene Ontology (GO) - Molecular Function for SIPA1L3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with SIPA1L3: view
genes like me logo Genes that share phenotypes with SIPA1L3: view

Human Phenotype Ontology for SIPA1L3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SIPA1L3

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SIPA1L3 Gene

Localization for SIPA1L3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIPA1L3 Gene

Apical cell membrane. Note=Detected in tricellular junctions. Colocalizes with apical F-actin. {ECO:0000269 PubMed:26231217}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SIPA1L3 gene
Compartment Confidence
cytoskeleton 5
plasma membrane 3
cytosol 3
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (2)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SIPA1L3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 stress fiber IDA 26231217
GO:0005615 extracellular space HDA 22664934
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016324 apical plasma membrane IEA --
genes like me logo Genes that share ontologies with SIPA1L3: view

Pathways & Interactions for SIPA1L3 Gene

PathCards logo

SuperPathways for SIPA1L3 Gene

SuperPathway Contained pathways
1 Ras signaling pathway
genes like me logo Genes that share pathways with SIPA1L3: view

Pathways by source for SIPA1L3 Gene

1 KEGG pathway for SIPA1L3 Gene

Gene Ontology (GO) - Biological Process for SIPA1L3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001654 eye development ISS --
GO:0002244 hematopoietic progenitor cell differentiation IEA --
GO:0003382 epithelial cell morphogenesis IDA,IEA 26231217
GO:0007010 cytoskeleton organization ISS,IEA --
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with SIPA1L3: view

No data available for SIGNOR curated interactions for SIPA1L3 Gene

Drugs & Compounds for SIPA1L3 Gene

No Compound Related Data Available

Transcripts for SIPA1L3 Gene

mRNA/cDNA for SIPA1L3 Gene

Unigene Clusters for SIPA1L3 Gene

Signal-induced proliferation-associated 1 like 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SIPA1L3

Alternative Splicing Database (ASD) splice patterns (SP) for SIPA1L3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22
SP1: - - -

Relevant External Links for SIPA1L3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SIPA1L3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SIPA1L3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SIPA1L3 Gene

This gene is overexpressed in Liver, secretome (30.2), Islet of Langerhans (8.2), Retina (8.1), Pancreas (6.7), and Monocytes (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SIPA1L3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SIPA1L3 Gene:


SOURCE GeneReport for Unigene cluster for SIPA1L3 Gene:


Evidence on tissue expression from TISSUES for SIPA1L3 Gene

  • Nervous system(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with SIPA1L3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SIPA1L3 Gene

Orthologs for SIPA1L3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SIPA1L3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SIPA1L3 35 34
  • 99.12 (n)
(Canis familiaris)
Mammalia SIPA1L3 35 34
  • 89.58 (n)
(Bos Taurus)
Mammalia SIPA1L3 35 34
  • 89.01 (n)
(Mus musculus)
Mammalia Sipa1l3 17 35 34
  • 86.41 (n)
(Monodelphis domestica)
Mammalia SIPA1L3 35
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia SIPA1L3 35
  • 67 (a)
(Anolis carolinensis)
Reptilia SIPA1L3 35
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sipa1l3 34
  • 64.69 (n)
Str.10258 34
(Danio rerio)
Actinopterygii si:dkey-149j18.1 34
  • 61.41 (n)
CABZ01030262.1 35
  • 34 (a)
Species where no ortholog for SIPA1L3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SIPA1L3 Gene

Gene Tree for SIPA1L3 (if available)
Gene Tree for SIPA1L3 (if available)
Evolutionary constrained regions (ECRs) for SIPA1L3: view image

Paralogs for SIPA1L3 Gene

Paralogs for SIPA1L3 Gene

(31) SIMAP similar genes for SIPA1L3 Gene using alignment to 7 proteins:

  • M0QX89_HUMAN
  • M0R185_HUMAN
  • M0R2Q7_HUMAN
  • M0R2W1_HUMAN
genes like me logo Genes that share paralogs with SIPA1L3: view

Variants for SIPA1L3 Gene

Sequence variations from dbSNP and Humsavar for SIPA1L3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs138476311 uncertain-significance, not provided, - 38,082,007(+) G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs756898971 pathogenic, Cataract 45 38,192,203(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, stop_gained
rs386352360 uncertain-significance, not provided 38,164,733(+) C/G/T coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, synonymous_variant
rs1000000426 -- 38,069,600(+) C/T intron_variant
rs1000002461 -- 38,101,896(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SIPA1L3 Gene

Variant ID Type Subtype PubMed ID
esv1080341 CNV insertion 17803354
esv2610413 CNV deletion 19546169
esv2658332 CNV deletion 23128226
esv2670217 CNV deletion 23128226
esv2718531 CNV deletion 23290073
esv3440280 CNV duplication 20981092
esv3583379 CNV loss 25503493
esv3644299 CNV loss 21293372
esv3644300 CNV loss 21293372
esv3644301 CNV loss 21293372
esv3644303 CNV loss 21293372
esv3644304 CNV loss 21293372
esv3644305 CNV loss 21293372
nsv1060359 CNV loss 25217958
nsv1062518 CNV loss 25217958
nsv1064401 CNV loss 25217958
nsv1109193 CNV deletion 24896259
nsv1123252 CNV deletion 24896259
nsv1127681 CNV deletion 24896259
nsv138463 CNV deletion 16902084
nsv472850 CNV novel sequence insertion 20440878
nsv474062 CNV novel sequence insertion 20440878
nsv833820 CNV loss 17160897
nsv833821 CNV loss 17160897
nsv954662 CNV deletion 24416366

Variation tolerance for SIPA1L3 Gene

Residual Variation Intolerance Score: 79.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.67; 82.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SIPA1L3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIPA1L3 Gene

Disorders for SIPA1L3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SIPA1L3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
cataract 45
  • ctrct45
cataract 44
  • ctrct44
  • cataracts
- elite association - COSMIC cancer census association via MalaCards


  • Note=A chromosomal translocation involving SIPA1L3 is found in a patient with bilateral severe ocular abnormalities including congenital cataracts, corneal clouding, iridocorneal and lenticular adhesions and microphthalmia. Chromosomal translocation t(2;19)(q37.3;q13.1). In addition to translocation, missense variant has been found in patient with bilateral congenital cataracts (PubMed:26231217). {ECO:0000269 PubMed:26231217}.
  • Cataract 45 (CTRCT45) [MIM:616851]: An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. {ECO:0000269 PubMed:25804400}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SIPA1L3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SIPA1L3: view

No data available for Genatlas for SIPA1L3 Gene

Publications for SIPA1L3 Gene

  1. SIPA1L3 identified by linkage analysis and whole-exome sequencing as a novel gene for autosomal recessive congenital cataract. (PMID: 25804400) Evers C … Moog U (European journal of human genetics : EJHG 2015) 3 4 58
  2. Mutations in SIPA1L3 cause eye defects through disruption of cell polarity and cytoskeleton organization. (PMID: 26231217) Greenlees R … Jamieson RV (Human molecular genetics 2015) 3 4 58
  3. RapGAPs in brain: multipurpose players in neuronal Rap signalling. (PMID: 20576033) Spilker C … Kreutz MR (The European journal of neuroscience 2010) 2 3 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 58
  5. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D … Nagase T (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 3 4 58

Products for SIPA1L3 Gene

Sources for SIPA1L3 Gene

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