SIPA1L2

gene
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Also known as KIAA1389SPAR2

Summary

SIPA1L2 (signal induced proliferation associated 1 like 2, HGNC:23800) is a protein-coding gene on chromosome 1q42.2, encoding Signal-induced proliferation-associated 1-like protein 2 (Q9P2F8).

This gene encodes a member of the signal-induced proliferation-associated 1 like family. Members of this family contain a GTPase activating domain, a PDZ domain and a C-terminal coiled-coil domain with a leucine zipper. A similar protein in rat acts as a GTPases for the small GTPase Rap.

Source: NCBI Gene 57568 — RefSeq curated summary.

At a glance

  • GWAS associations: 15
  • Clinical variants (ClinVar): 285 total
  • MANE Select transcript: NM_020808

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23800
Approved symbolSIPA1L2
Namesignal induced proliferation associated 1 like 2
Location1q42.2
Locus typegene with protein product
StatusApproved
AliasesKIAA1389, SPAR2
Ensembl geneENSG00000116991
Ensembl biotypeprotein_coding
OMIM611609
Entrez57568

Gene structure

Transcript identifiers

Ensembl transcripts: 47 — 43 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000308942, ENST00000366630, ENST00000486472, ENST00000494056, ENST00000495863, ENST00000674635, ENST00000674749, ENST00000674801, ENST00000675407, ENST00000675685, ENST00000676213, ENST00000883504, ENST00000883505, ENST00000883506, ENST00000883507, ENST00000883508, ENST00000883509, ENST00000883510, ENST00000930079, ENST00000930080, ENST00000930081, ENST00000930082, ENST00000930083, ENST00000930084, ENST00000930085, ENST00000964474, ENST00000964475, ENST00000964476, ENST00000964477, ENST00000964478, ENST00000964479, ENST00000964480, ENST00000964481, ENST00000964482, ENST00000964483, ENST00000964484, ENST00000964485, ENST00000964486, ENST00000964487, ENST00000964488, ENST00000964489, ENST00000964490, ENST00000964491, ENST00000964492, ENST00000964493, ENST00000964494, ENST00000964495

RefSeq mRNA: 2 — MANE Select: NM_020808 NM_001377488, NM_020808

CCDS: CCDS41474, CCDS91174

Canonical transcript exons

ENST00000674635 — 23 exons

ExonStartEnd
ENSE00000793231232415494232415625
ENSE00000793232232425589232425808
ENSE00000805300232428411232428564
ENSE00000805303232460887232461161
ENSE00000921398232402392232402473
ENSE00000921399232403448232403571
ENSE00000921400232404125232404178
ENSE00000921401232432247232432471
ENSE00000921402232439108232439496
ENSE00000921408232483792232483966
ENSE00000921409232490874232491062
ENSE00001176131232441291232441394
ENSE00001176138232441768232441868
ENSE00001176143232443602232443685
ENSE00001176150232445529232445786
ENSE00001176160232464840232465416
ENSE00001442210232397965232399273
ENSE00001442211232513857232515608
ENSE00001796126232479627232479730
ENSE00002220003232471371232471528
ENSE00003560550232493527232493660
ENSE00003900808232574174232574222
ENSE00003901320232629869232630133

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 98.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.8887 / max 98.9565, expressed in 1035 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
180104.4163999
2019930.4392263
180090.033210

Top tissues by expression

258 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
left ventricle myocardiumUBERON:000656698.81gold quality
cardiac muscle of right atriumUBERON:000337998.56gold quality
ponsUBERON:000098897.59gold quality
deciduaUBERON:000245097.57gold quality
heart right ventricleUBERON:000208097.40gold quality
myocardiumUBERON:000234997.09gold quality
lateral nuclear group of thalamusUBERON:000273696.41gold quality
buccal mucosa cellCL:000233696.20gold quality
middle temporal gyrusUBERON:000277195.75gold quality
sural nerveUBERON:001548895.75gold quality
substantia nigra pars compactaUBERON:000196594.99gold quality
substantia nigra pars reticulataUBERON:000196694.61gold quality
endothelial cellCL:000011594.27gold quality
trigeminal ganglionUBERON:000167593.88gold quality
epithelial cell of pancreasCL:000008393.77gold quality
tibialis anteriorUBERON:000138593.55gold quality
Brodmann (1909) area 23UBERON:001355493.41gold quality
dorsal root ganglionUBERON:000004493.26gold quality
visceral pleuraUBERON:000240193.06gold quality
secondary oocyteCL:000065592.97gold quality
lower esophagus mucosaUBERON:003583492.81gold quality
cardiac ventricleUBERON:000208291.86gold quality
esophagus squamous epitheliumUBERON:000692091.85gold quality
cardiac atriumUBERON:000208191.84gold quality
heart left ventricleUBERON:000208491.71gold quality
tendon of biceps brachiiUBERON:000818891.65gold quality
oocyteCL:000002391.64gold quality
Brodmann (1909) area 46UBERON:000648391.58gold quality
superior vestibular nucleusUBERON:000722791.55gold quality
tibial nerveUBERON:000132391.43gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-CURD-119yes24.00
E-ENAD-27yes10.31
E-ANND-3yes5.87
E-MTAB-7303no197.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

146 targeting SIPA1L2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4262100.0073.263931
HSA-MIR-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-4692100.0067.322066
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-428299.9975.366408
HSA-MIR-451499.9967.101870
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-548P99.9872.253784
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-493-5P99.9672.472382
HSA-LET-7C-3P99.9573.422862
HSA-MIR-767-5P99.9570.85993
HSA-MIR-391099.9571.132227
HSA-MIR-545-3P99.9570.742783
HSA-MIR-55999.9572.283609
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-314399.9371.963104

Literature-anchored findings (GeneRIF, showing 2)

  • Our results suggest that rs329648 is associated with risk of developing PD in the Han Chinese population. Our findings should be verified in further studies, and they highlight the need for functional studies of MIR4697. (PMID:28380328)
  • SIPA1L2 is a potential genetic modifier of CMT1A phenotypic expressions. (PMID:30706531)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosipa1l2ENSDARG00000061640
mus_musculusSipa1l2ENSMUSG00000001995
rattus_norvegicusSipa1l2ENSRNOG00000019791
drosophila_melanogasterRapGAP1FBGN0264895
caenorhabditis_elegansWBGENE00018734

Paralogs (6): RAP1GAP (ENSG00000076864), SIPA1L3 (ENSG00000105738), RAP1GAP2 (ENSG00000132359), GARNL3 (ENSG00000136895), SIPA1L1 (ENSG00000197555), SIPA1 (ENSG00000213445)

Protein

Protein identifiers

Signal-induced proliferation-associated 1-like protein 2Q9P2F8 (reviewed: Q9P2F8)

All UniProt accessions (4): A0A6Q8PFQ0, A0A6Q8PGD5, A0A6Q8PH54, Q9P2F8

Isoforms (2)

UniProt IDNamesCanonical?
Q9P2F8-11yes
Q9P2F8-22

RefSeq proteins (2): NP_001364417, NP_065859* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000331Rap/Ran_GAP_domDomain
IPR001478PDZDomain
IPR021818SIPA1L_CDomain
IPR035974Rap/Ran-GAP_sfHomologous_superfamily
IPR036034PDZ_sfHomologous_superfamily
IPR050989Rap1_Ran_GAPFamily

Pfam: PF00595, PF02145, PF11881, PF21022

UniProt features (42 total): modified residue 12, compositionally biased region 10, region of interest 5, sequence variant 5, splice variant 3, sequence conflict 3, domain 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P2F8-F156.590.24

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (12): 148, 379, 383, 1029, 1244, 1461, 1472, 1478, 1488, 1549, 1552, 1591

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 192 (showing top): WHITEHURST_PACLITAXEL_SENSITIVITY, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, PEREZ_TP63_TARGETS, GOZGIT_ESR1_TARGETS_DN, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GTTAAAG_MIR302B, ATGTTAA_MIR302C, WANG_LMO4_TARGETS_DN, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, PEREZ_TP53_AND_TP63_TARGETS, CTTTGTA_MIR524, MODULE_207, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION

GO Biological Process (3): regulation of small GTPase mediated signal transduction (GO:0051056), presynaptic signal transduction (GO:0098928), biological_process (GO:0008150)

GO Molecular Function (2): GTPase activator activity (GO:0005096), protein binding (GO:0005515)

GO Cellular Component (3): cytoplasm (GO:0005737), glutamatergic synapse (GO:0098978), cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
small GTPase-mediated signal transduction1
regulation of intracellular signal transduction1
signal transduction1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
binding1
intracellular anatomical structure1
cellular anatomical structure1
synapse1

Protein interactions and networks

STRING

778 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SIPA1L2SNAPINO95295614
SIPA1L2PRR35P0CG20576
SIPA1L2DDRGK1Q96HY6567
SIPA1L2VPS13CQ709C8544
SIPA1L2KBTBD12Q3ZCT8523
SIPA1L2RIT2Q99578507
SIPA1L2RRP36Q96EU6493
SIPA1L2SPMIP7A4D263472
SIPA1L2KLHDC8BQ8IXV7472
SIPA1L2TOGARAM1Q9Y4F4469
SIPA1L2IHO1Q8IYA8455
SIPA1L2KCNG3Q8TAE7450
SIPA1L2VWC2Q2TAL6445
SIPA1L2LZTS3O60299443
SIPA1L2PKDCCQ504Y2437

IntAct

525 interactions, top by confidence:

ABTypeScore
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
PRG2YPEL5psi-mi:“MI:0914”(association)0.640
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
ESIPA1L2psi-mi:“MI:0915”(physical association)0.610
YWHABBLTP3Bpsi-mi:“MI:2364”(proximity)0.610
ESIPA1L2psi-mi:“MI:0407”(direct interaction)0.610
SIPA1L2E6psi-mi:“MI:0915”(physical association)0.590
E6SIPA1L2psi-mi:“MI:0407”(direct interaction)0.590
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
TSPYL1GPC3psi-mi:“MI:0914”(association)0.530
YWHAQIGLC7psi-mi:“MI:0914”(association)0.530
YWHABSHTN1psi-mi:“MI:0914”(association)0.530
YWHAESHTN1psi-mi:“MI:0914”(association)0.530
YWHAZSHTN1psi-mi:“MI:0914”(association)0.530
YWHAZBLTP3Bpsi-mi:“MI:0914”(association)0.530
DYRK1BBMAL1psi-mi:“MI:0914”(association)0.530
GNG4SIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
CREBBPSIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
E6SIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
TaxSIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
NET1SIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
PTENSIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
RPS6KA1SIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
ESIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
GP1SIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
ABCA1SIPA1L2psi-mi:“MI:0407”(direct interaction)0.440
ABRAXAS2SIPA1L2psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (173): SIPA1L2 (Two-hybrid), SIPA1L2 (Affinity Capture-MS), SIPA1L2 (Affinity Capture-MS), SIPA1L2 (Affinity Capture-MS), SIPA1L2 (Proximity Label-MS), SIPA1L2 (Proximity Label-MS), SIPA1L2 (Proximity Label-MS), SIPA1L2 (Proximity Label-MS), SIPA1L2 (Proximity Label-MS), SIPA1L2 (Proximity Label-MS), SIPA1L2 (Affinity Capture-MS), SIPA1L2 (Affinity Capture-MS), SIPA1L2 (Affinity Capture-MS), SIPA1L2 (Affinity Capture-MS), SIPA1L2 (Affinity Capture-MS)

ESM2 similar proteins: A1A5R8, A8KBE0, B4F6Q9, E7FA21, O43166, P53804, P62287, P62289, P62290, P62291, P62292, P62293, P62294, Q06190, Q08AX9, Q0VA42, Q12923, Q13829, Q3UMB5, Q5F3E8, Q5JCS6, Q5RA75, Q5RBH4, Q5TB30, Q5XKL5, Q5ZIX8, Q65Z40, Q68FF0, Q6DJS0, Q6GQJ2, Q6IE81, Q6ING4, Q6IRN6, Q6NPP4, Q6NSI8, Q6PUR7, Q7Z5K2, Q7ZXG4, Q8C0T5, Q8CIG0

Diamond homologs: A2ALS5, A5PF44, G3X9J0, O35412, O43166, O60292, P46062, P47736, P49815, P49816, Q3V0G7, Q54EH3, Q55AN8, Q5JCS6, Q5SVL6, Q5VVW2, Q5ZJY3, Q5ZMV8, Q61037, Q684P5, Q75J96, Q80TE4, Q8C0T5, Q96FS4, Q9P2F8, Q2PPJ7, Q9UUG9, A3KGS3, P86411, Q6GYQ0, Q8BUL6, Q9HB21, Q54TK4, Q9VB98, O55007, Q6GYP7, Q54SS8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 178 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Activation of BAD and translocation to mitochondria747.2×8e-09
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex741.6×2e-08
SARS-CoV-1 targets host intracellular signalling and regulatory pathways741.6×2e-08
Activation of BH3-only proteins730.8×1e-07
RHO GTPases activate PKNs719.6×4e-06
Intrinsic Pathway for Apoptosis718.1×5e-06
FOXO-mediated transcription617.8×4e-05
Transcriptional and post-translational regulation of MITF-M expression and activity812.6×1e-05

GO biological processes:

GO termPartnersFoldFDR
intracellular protein localization106.6×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

285 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance240
Likely benign13
Benign10

Top pathogenic / likely-pathogenic (0)

SpliceAI

4049 predictions. Top by Δscore:

VariantEffectΔscore
1:232402379:T:TAdonor_gain1.0000
1:232402387:ATTAC:Adonor_loss1.0000
1:232402388:TTACC:Tdonor_loss1.0000
1:232402389:TACCT:Tdonor_loss1.0000
1:232402391:C:CTdonor_loss1.0000
1:232402394:T:Adonor_gain1.0000
1:232403572:C:CCacceptor_gain1.0000
1:232415488:CTTTA:Cdonor_loss1.0000
1:232415489:TTTA:Tdonor_loss1.0000
1:232415490:TTA:Tdonor_loss1.0000
1:232415491:TACC:Tdonor_loss1.0000
1:232415621:CTCAT:Cacceptor_gain1.0000
1:232415622:TCAT:Tacceptor_gain1.0000
1:232415623:CAT:Cacceptor_gain1.0000
1:232415623:CATC:Cacceptor_gain1.0000
1:232415625:TC:Tacceptor_loss1.0000
1:232415626:C:CCacceptor_gain1.0000
1:232425587:A:ACdonor_gain1.0000
1:232425588:C:CCdonor_gain1.0000
1:232425588:CTTCT:Cdonor_gain1.0000
1:232425796:C:Tacceptor_gain1.0000
1:232428406:CTAA:Cdonor_loss1.0000
1:232428407:TAA:Tdonor_loss1.0000
1:232428408:AACCT:Adonor_loss1.0000
1:232428409:A:AGdonor_loss1.0000
1:232428561:CATC:Cacceptor_gain1.0000
1:232428565:C:CCacceptor_gain1.0000
1:232439102:GCTTA:Gdonor_loss1.0000
1:232439103:CTTA:Cdonor_loss1.0000
1:232439104:TTA:Tdonor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000001614 (1:232614767 AG>A), RS1000006790 (1:232447231 T>C), RS1000016017 (1:232573904 G>A), RS1000035190 (1:232447424 A>C), RS1000056111 (1:232569168 T>C), RS1000077031 (1:232534839 CCT>C), RS1000093375 (1:232575966 G>A), RS1000150365 (1:232478707 T>C), RS1000160385 (1:232474256 G>A), RS1000173515 (1:232609190 T>C), RS1000175947 (1:232467498 G>A,C), RS1000179553 (1:232505657 C>T), RS1000210677 (1:232625837 T>C), RS1000224110 (1:232608919 A>G), RS1000230954 (1:232563309 T>C)

Disease associations

OMIM: gene MIM:611609 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

15 associations (top):

StudyTraitp-value
GCST000763_1Immunoglobulin A1.000000e-06
GCST002361_17Smooth-surface caries8.000000e-06
GCST002401_1Post-traumatic stress disorder8.000000e-06
GCST002544_12Parkinson’s disease5.000000e-10
GCST004902_41Parkinson’s disease8.000000e-13
GCST007205_7Schizophrenia1.000000e-06
GCST007304_1Reduced foot dorsiflexion strength in Charcot-Marie-Tooth disease type 1A6.000000e-08
GCST009325_85Parkinson’s disease or first degree relation to individual with Parkinson’s disease7.000000e-17
GCST010320_119PR interval3.000000e-14
GCST010321_183PR interval3.000000e-15
GCST010989_191Body size at age 107.000000e-09
GCST010991_27Parkinson’s disease2.000000e-07
GCST011696_5Alzheimer’s disease6.000000e-07
GCST012307_3Bipolar disorder x sex interaction2.000000e-06
GCST90000047_22Age at first sexual intercourse2.000000e-08

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004747protein measurement
EFO:0004462PR interval
EFO:0009819comparative body size at age 10, self-reported
EFO:0008343sex interaction measurement
EFO:0009749age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

72 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, decreases methylation4
Valproic Aciddecreases expression, increases expression4
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression, increases expression3
sodium arsenitedecreases expression, increases expression2
potassium chromate(VI)affects cotreatment, decreases expression2
mercuric bromideaffects cotreatment, increases expression2
(+)-JQ1 compoundincreases expression2
Benzo(a)pyreneincreases expression2
Cisplatinaffects expression2
Estradiolaffects cotreatment, increases expression, decreases reaction2
Ethinyl Estradiolaffects expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tretinoindecreases expression, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
mivebresibincreases expression1
2,4,6-tribromophenoldecreases expression1
chloroacetaldehydedecreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
2,5,2’,5’-tetrachlorobiphenylincreases expression1
decabromobiphenyl etherdecreases expression1
trichostatin Aincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chloridedecreases expression1
tetrabromobisphenol Adecreases expression1
diallyl trisulfidedecreases expression1
beta-methylcholineaffects expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.