SIPA1L3 signal induced proliferation associated 1 like 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SIPA1L3provided by HGNC
Official Full Name: signal induced proliferation associated 1 like 3provided by HGNC
Primary source: HGNC:HGNC:23801
See related: Ensembl:ENSG00000105738 MIM:616655; AllianceGenome:HGNC:23801
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SPAL3; SPAR3; CTRCT45
Summary: 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]
Expression: Ubiquitous expression in small intestine (RPKM 6.9), duodenum (RPKM 6.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.13-q13.2

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (37907208..38208369)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (40709260..41010527)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (38397848..38699009)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

smoking cessation benefited survival of LUAD patients with low methylation at cg02268510SIPA 1L3 . The results have implications for not only smoking cessation after diagnosis, but also possible methylation-specific drug targeting.
Title: SIPA1L3 methylation modifies the benefit of smoking cessation on lung adenocarcinoma survival: an epigenomic-smoking interaction analysis.
Whole-exome sequencing identified a homozygous nonsense variant in SIPA1L3 in two sisters with congenital cataract.
Title: SIPA1L3 identified by linkage analysis and whole-exome sequencing as a novel gene for autosomal recessive congenital cataract.
Abnormalities of SIPA1L3 contribute to lens and eye defects, and we identify a critical role for SIPA1L3 in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organization.
Title: Mutations in SIPA1L3 cause eye defects through disruption of cell polarity and cytoskeleton organization.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Cataract 45 MedGen: C4225182 OMIM: 616851 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SIPA1L3__6837 (e-PCR)
- UniSTS:466433

STS-T56936 (e-PCR)
- UniSTS:65862

D19S228 (e-PCR), detects polymorphism
- UniSTS:13655

D19S220 (e-PCR), detects polymorphism
- UniSTS:20334

SHGC-148608 (e-PCR)
- UniSTS:176495

D19S557 (e-PCR)
- UniSTS:44146

D19S228 (e-PCR), detects polymorphism
- UniSTS:59797

RH48216 (e-PCR)
- UniSTS:10647

SHGC-111541 (e-PCR)
- UniSTS:168388

D19S228 (e-PCR), detects polymorphism
- UniSTS:7395

D19S1069 (e-PCR)
- UniSTS:34299

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in epithelial cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in epithelial cell morphogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in establishment of epithelial cell polarity	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of epithelial cell polarity	IDA Inferred from Direct Assay more info	PubMed
involved_in eye development	ISS Inferred from Sequence or Structural Similarity more info
involved_in hematopoietic progenitor cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of small GTPase mediated signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in apical part of cell	IMP Inferred from Mutant Phenotype more info	PubMed
located_in apical plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	HDA more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in postsynaptic specialization, intracellular component	IEA Inferred from Electronic Annotation more info
located_in stress fiber	IDA Inferred from Direct Assay more info	PubMed
located_in tricellular tight junction	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: signal-induced proliferation-associated 1-like protein 3

Names: SIPA1-like protein 3; SPA-1-like protein 3; spine-associated RapGAP 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_046730.1 RefSeqGene

Range

4988..306149

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_015073.3 → NP_055888.1 signal-induced proliferation-associated 1-like protein 3

See identical proteins and their annotated locations for NP_055888.1

Status: REVIEWED

Source sequence(s)

AC011465, AC011479, AC016582, AI560928, BC150620, BM193478

Consensus CDS

CCDS33007.1

UniProtKB/Swiss-Prot

O60292, Q2TV87

Related

ENSP00000222345.4, ENST00000222345.11

Conserved Domains (3) summary

cd00992
Location:966 → 1036

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam02145
Location:641 → 821

Rap_GAP; Rap/ran-GAP

pfam11881
Location:1477 → 1726

SPAR_C; C-terminal domain of SPAR protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

37907208..38208369

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047438486.1 → XP_047294442.1 signal-induced proliferation-associated 1-like protein 3 isoform X1

UniProtKB/Swiss-Prot

O60292, Q2TV87
XM_017026518.3 → XP_016882007.1 signal-induced proliferation-associated 1-like protein 3 isoform X2

Conserved Domains (3) summary

cd00992
Location:966 → 1036

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam02145
Location:641 → 821

Rap_GAP; Rap/ran-GAP

pfam11881
Location:1477 → 1725

SPAR_C; C-terminal domain of SPAR protein
XM_047438490.1 → XP_047294446.1 signal-induced proliferation-associated 1-like protein 3 isoform X3
XM_047438489.1 → XP_047294445.1 signal-induced proliferation-associated 1-like protein 3 isoform X1

UniProtKB/Swiss-Prot

O60292, Q2TV87
XM_047438487.1 → XP_047294443.1 signal-induced proliferation-associated 1-like protein 3 isoform X1

UniProtKB/Swiss-Prot

O60292, Q2TV87
XM_011526657.3 → XP_011524959.1 signal-induced proliferation-associated 1-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_011524959.1

UniProtKB/Swiss-Prot

O60292, Q2TV87

Conserved Domains (3) summary

cd00992
Location:966 → 1036

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam02145
Location:641 → 821

Rap_GAP; Rap/ran-GAP

pfam11881
Location:1477 → 1726

SPAR_C; C-terminal domain of SPAR protein
XM_047438488.1 → XP_047294444.1 signal-induced proliferation-associated 1-like protein 3 isoform X1

UniProtKB/Swiss-Prot

O60292, Q2TV87

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

40709260..41010527

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054320310.1 → XP_054176285.1 signal-induced proliferation-associated 1-like protein 3 isoform X2
XM_054320311.1 → XP_054176286.1 signal-induced proliferation-associated 1-like protein 3 isoform X3
XM_054320308.1 → XP_054176283.1 signal-induced proliferation-associated 1-like protein 3 isoform X1

UniProtKB/TrEMBL

B2RWP0
XM_054320309.1 → XP_054176284.1 signal-induced proliferation-associated 1-like protein 3 isoform X1

UniProtKB/TrEMBL

B2RWP0