SYNPO2L

gene
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Also known as FLJ12921

Summary

SYNPO2L (synaptopodin 2 like, HGNC:23532) is a protein-coding gene on chromosome 10q22.2, encoding Synaptopodin 2-like protein (Q9H987). Actin-associated protein that may play a role in modulating actin-based shape.

Predicted to enable actin binding activity. Predicted to be involved in several processes, including positive regulation of Rho protein signal transduction; positive regulation of stress fiber assembly; and sarcomere organization. Predicted to be located in cytoplasm and cytoskeleton. Predicted to be active in Z disc; actin cytoskeleton; and nucleus.

Source: NCBI Gene 79933 — RefSeq curated summary.

At a glance

  • GWAS associations: 25
  • Clinical variants (ClinVar): 141 total
  • MANE Select transcript: NM_001114133

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23532
Approved symbolSYNPO2L
Namesynaptopodin 2 like
Location10q22.2
Locus typegene with protein product
StatusApproved
AliasesFLJ12921
Ensembl geneENSG00000166317
Ensembl biotypeprotein_coding
Entrez79933

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000372873, ENST00000394810, ENST00000606523

RefSeq mRNA: 2 — MANE Select: NM_001114133 NM_001114133, NM_024875

CCDS: CCDS44438, CCDS7331

Canonical transcript exons

ENST00000394810 — 4 exons

ExonStartEnd
ENSE000014588607365313973653653
ENSE000014588617365412973654280
ENSE000015196567365581873656029
ENSE000038472697364488673648879

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 98.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.5287 / max 236.8828, expressed in 158 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1100990.777478
1100940.436198
1101010.251943
1100960.01748
1100950.016910
1101000.015512
1101020.01356

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
skeletal muscle tissue of rectus abdominisUBERON:000451198.87gold quality
apex of heartUBERON:000209898.85gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.42gold quality
biceps brachiiUBERON:000150798.40gold quality
vastus lateralisUBERON:000137998.04gold quality
heart right ventricleUBERON:000208097.92gold quality
myocardiumUBERON:000234997.79gold quality
cardiac muscle of right atriumUBERON:000337997.75gold quality
left ventricle myocardiumUBERON:000656697.65gold quality
quadriceps femorisUBERON:000137797.61gold quality
gluteal muscleUBERON:000200097.50gold quality
skeletal muscle tissueUBERON:000113497.07gold quality
body of tongueUBERON:001187696.99gold quality
hindlimb stylopod muscleUBERON:000425296.95gold quality
cardiac atriumUBERON:000208196.93gold quality
cardiac ventricleUBERON:000208296.90gold quality
heart left ventricleUBERON:000208496.85gold quality
right atrium auricular regionUBERON:000663196.75gold quality
gastrocnemiusUBERON:000138896.51gold quality
vena cavaUBERON:000408796.33gold quality
deltoidUBERON:000147695.90gold quality
muscle organUBERON:000163095.75gold quality
tibialis anteriorUBERON:000138595.07gold quality
muscle of legUBERON:000138395.04gold quality
triceps brachiiUBERON:000150994.87gold quality
muscle tissueUBERON:000238593.61gold quality
heartUBERON:000094892.58gold quality
tongueUBERON:000172389.88gold quality
lower esophagus mucosaUBERON:003583487.19gold quality
superior surface of tongueUBERON:000737185.67gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

95 targeting SYNPO2L, 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-8485100.0077.574731
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-150-5P99.9966.691976
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-450099.9972.722367
HSA-MIR-806899.9873.852376
HSA-MIR-651-3P99.9473.485177
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-454-3P99.9174.011925
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-444799.8567.812900
HSA-MIR-629-3P99.8567.991875
HSA-MIR-202-3P99.8471.411290
HSA-MIR-6715A-3P99.8368.051473
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-4639-5P99.8167.371028
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-674599.7465.331321
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-29B-2-5P99.6768.981726
HSA-MIR-509399.6769.262291
HSA-MIR-10393-5P99.6568.011368
HSA-MIR-6848-3P99.6466.49885
HSA-MIR-29899.6367.561916
HSA-MIR-4756-3P99.6266.301319
HSA-MIR-451699.6167.783390

Literature-anchored findings (GeneRIF, showing 2)

  • we did not observe associations between coding genetic variants and Atrial fibrillation (AF), suggesting that large-effect coding variation is not the predominant mechanism underlying AF. A coding variant in SYNPO2L requires further evaluation to determine whether it is causally related to AF (PMID:27589061)
  • METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts. (PMID:39247832)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosynpo2laENSDARG00000077293
danio_reriosynpo2lbENSDARG00000078696
mus_musculusSynpo2lENSMUSG00000039376
rattus_norvegicusSynpo2lENSRNOG00000008949
drosophila_melanogasterCG1674FBGN0039897

Paralogs (2): SYNPO (ENSG00000171992), SYNPO2 (ENSG00000172403)

Protein

Protein identifiers

Synaptopodin 2-like proteinQ9H987 (reviewed: Q9H987)

All UniProt accessions (2): Q9H987, U3KQD0

UniProt curated annotations — full annotation on UniProt →

Function. Actin-associated protein that may play a role in modulating actin-based shape.

Subcellular location. Cytoplasm. Cytoskeleton.

Similarity. Belongs to the synaptopodin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H987-11yes
Q9H987-22

RefSeq proteins (2): NP_001107605, NP_079151 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001478PDZDomain
IPR036034PDZ_sfHomologous_superfamily
IPR051976Synaptopodin_domainFamily

Pfam: PF00595

UniProt features (59 total): modified residue 34, compositionally biased region 12, region of interest 5, sequence variant 3, splice variant 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H987-F153.100.12

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 (34): 108, 111, 141, 143, 178, 180, 345, 350, 374, 381, 384, 386, 466, 469, 479, 670, 678, 705, 713, 757 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, MYOGENIN_Q6, GOBP_POSITIVE_REGULATION_OF_RHO_PROTEIN_SIGNAL_TRANSDUCTION, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, MEF2_02, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_SARCOMERE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, GNF2_MYL3, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP, GOBP_ANIMAL_ORGAN_MORPHOGENESIS

GO Biological Process (5): heart morphogenesis (GO:0003007), positive regulation of actin filament bundle assembly (GO:0032233), positive regulation of Rho protein signal transduction (GO:0035025), sarcomere organization (GO:0045214), positive regulation of stress fiber assembly (GO:0051496)

GO Molecular Function (2): actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), actin cytoskeleton (GO:0015629), Z disc (GO:0030018), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), organelle (GO:0043226)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
heart development1
animal organ morphogenesis1
regulation of actin filament bundle assembly1
positive regulation of cellular component biogenesis1
actin filament bundle assembly1
positive regulation of cytoskeleton organization1
positive regulation of supramolecular fiber organization1
Rho protein signal transduction1
regulation of Rho protein signal transduction1
positive regulation of small GTPase mediated signal transduction1
myofibril assembly1
actomyosin structure organization1
positive regulation of actin filament bundle assembly1
stress fiber assembly1
regulation of stress fiber assembly1
cytoskeletal protein binding1
binding1
intracellular membrane-bounded organelle1
cytoskeleton1
I band1
intracellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

858 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYNPO2LZFHX3Q15911692
SYNPO2LMYOZ1Q9NP98677
SYNPO2LAOPEPQ8N6M6608
SYNPO2LSYNE2Q8WXH0581
SYNPO2LCAND2O75155581
SYNPO2LTBX3O15119568
SYNPO2LHCN4Q9Y3Q4530
SYNPO2LPRRX1P54821512
SYNPO2LWDTC1Q8N5D0485
SYNPO2LPITX2Q99697479
SYNPO2LKCNN3Q9UGI6476
SYNPO2LNEURL1O76050471
SYNPO2LRPL3LQ92901434
SYNPO2LWNT8AQ9H1J5419
SYNPO2LCCDC197Q8NCU1400

IntAct

30 interactions, top by confidence:

ABTypeScore
ESYNPO2Lpsi-mi:“MI:0915”(physical association)0.590
ABCC4SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
ARHGEF16SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
ASIC3SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
ATP2B4SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
CYSLTR2SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
DGKKSYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
DGKZSYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
DOCK4SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
FRMPD4SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
FZD7SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
TAMALINSYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
E6SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
ORF putative E6SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
SYNPO2LE6psi-mi:“MI:0407”(direct interaction)0.440
KCNA5SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
KIR3DL3SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
MAP2K2SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
PBKSYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
RALBP1SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
RASSF6SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
SLC15A5SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
SLCO1C1SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
TJP2SYNPO2Lpsi-mi:“MI:0407”(direct interaction)0.440
SYNPO2LDlg4psi-mi:“MI:0407”(direct interaction)0.440
SYNPO2LTOMM20psi-mi:“MI:0915”(physical association)0.400
TBC1D2BCEP120psi-mi:“MI:0914”(association)0.350

BioGRID (12): SYNPO2L (Two-hybrid), SYNPO2L (Two-hybrid), SYNPO2L (Two-hybrid), SYNPO2L (Two-hybrid), SYNPO2L (Two-hybrid), GOLGA2 (Two-hybrid), ACTN3 (Two-hybrid), SYNPO2L (Proximity Label-MS), SYNPO2L (Affinity Capture-MS), SYNPO2L (Protein-peptide), SYNPO2L (Cross-Linking-MS (XL-MS)), SYNPO2L (Protein-peptide)

ESM2 similar proteins: D3ZQL6, D4A702, E7F568, E9Q0S6, O35867, O54916, O54931, P19973, Q08495, Q08DM1, Q09YM8, Q1LVV0, Q2MJV9, Q3UH68, Q3UIL6, Q4KM62, Q4PS85, Q5NBX1, Q5R4B6, Q5RBH3, Q5RG44, Q5RHU7, Q5U301, Q68CZ2, Q6P4R8, Q6PIJ4, Q80Z38, Q8BWB1, Q8C5R2, Q8CC35, Q8IVT2, Q8K382, Q8N3V7, Q91YE8, Q96D71, Q9D067, Q9D279, Q9GLM4, Q9H987, Q9HBL0

Diamond homologs: A1ZA47, A2ALU4, A5H447, D4A702, E1BKA3, O00151, O14639, O43294, O60711, O70209, O70400, O75112, O94929, P20271, P48059, P49023, P49024, P50464, P52944, Q09476, Q0WSN2, Q13796, Q15942, Q1JQB5, Q2KJ33, Q2TCH4, Q2YDK0, Q3MHZ4, Q3SX26, Q3SX40, Q3SYZ8, Q3T0X8, Q3TJD7, Q55BI0, Q5F464, Q5R7I1, Q5RCF7, Q5TD97, Q5U2Z2, Q5XI07

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance137
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1043 predictions. Top by Δscore:

VariantEffectΔscore
10:73654128:CCG:Cdonor_gain1.0000
10:73648880:C:CCacceptor_gain0.9900
10:73653138:CTGG:Cdonor_gain0.9900
10:73654155:T:TAdonor_gain0.9900
10:73654286:A:ACacceptor_gain0.9900
10:73654286:A:Cacceptor_gain0.9900
10:73648875:CAGTT:Cacceptor_gain0.9800
10:73648878:TTCTG:Tacceptor_loss0.9800
10:73648879:TCTGG:Tacceptor_loss0.9800
10:73648880:C:CAacceptor_loss0.9800
10:73648881:T:Aacceptor_loss0.9800
10:73655813:CTTAC:Cdonor_loss0.9800
10:73655814:TTAC:Tdonor_loss0.9800
10:73655816:A:Tdonor_loss0.9800
10:73655817:CCT:Cdonor_loss0.9800
10:73655929:G:Cdonor_gain0.9800
10:73648877:GTT:Gacceptor_gain0.9700
10:73650673:A:ACdonor_gain0.9700
10:73650674:C:CCdonor_gain0.9700
10:73650674:CACA:Cdonor_gain0.9700
10:73653137:A:ACdonor_gain0.9700
10:73653138:C:CCdonor_gain0.9700
10:73653316:CACGG:Cdonor_gain0.9700
10:73654127:A:ACdonor_gain0.9700
10:73654128:C:CCdonor_gain0.9700
10:73654280:TC:Tacceptor_loss0.9700
10:73654281:C:CGacceptor_loss0.9700
10:73654282:T:Gacceptor_loss0.9700
10:73654289:T:Cacceptor_gain0.9700
10:73654289:T:TCacceptor_gain0.9700

AlphaMissense

6176 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:73648758:A:CF298L1.000
10:73648758:A:TF298L1.000
10:73648759:A:GF298S1.000
10:73648760:A:GF298L1.000
10:73648759:A:CF298C0.999
10:73648801:A:GL284P0.999
10:73648801:A:TL284H0.999
10:73648804:A:GL283P0.999
10:73648813:A:TI280N0.999
10:73655867:A:GF19S0.999
10:73648747:C:GR302P0.998
10:73648760:A:CF298V0.998
10:73648760:A:TF298I0.998
10:73648772:C:GG294R0.998
10:73648772:C:TG294R0.998
10:73648813:A:CI280S0.998
10:73647257:A:GW799R0.997
10:73647257:A:TW799R0.997
10:73648740:T:AR304S0.997
10:73648740:T:GR304S0.997
10:73648765:A:GL296P0.997
10:73648773:T:AK293N0.997
10:73648773:T:GK293N0.997
10:73648811:C:GA281P0.997
10:73654246:A:GL47P0.997
10:73655866:G:CF19L0.997
10:73655866:G:TF19L0.997
10:73655868:A:GF19L0.997
10:73655874:A:GW17R0.997
10:73655874:A:TW17R0.997

dbSNP variants (sampled 300 via entrez): RS1000261009 (10:73648745 G>A), RS1000630062 (10:73646854 G>T), RS1000878347 (10:73656242 A>T), RS1001060689 (10:73653757 G>A), RS1001377793 (10:73652434 C>T), RS1001407150 (10:73651949 C>T), RS1001483278 (10:73651286 G>A), RS1002214390 (10:73650695 T>A), RS1002535213 (10:73652494 C>T), RS1002545069 (10:73652177 G>A), RS1002770334 (10:73657003 G>A), RS1002941839 (10:73657339 A>G,T), RS1003801727 (10:73647073 G>A,T), RS1003989254 (10:73649664 C>A,G), RS1004004429 (10:73656010 C>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

25 associations (top):

StudyTraitp-value
GCST001499_8Atrial fibrillation4.000000e-09
GCST004297_16Atrial fibrillation8.000000e-11
GCST004300_3Incident atrial fibrillation3.000000e-08
GCST005306_1Atrial fibrillation2.000000e-06
GCST006061_29Atrial fibrillation6.000000e-27
GCST006061_96Atrial fibrillation6.000000e-27
GCST006231_39Mean arterial pressure6.000000e-06
GCST006259_61Systolic blood pressure8.000000e-09
GCST006414_1Atrial fibrillation9.000000e-35
GCST007656_13Chronic obstructive pulmonary disease or resting heart rate (pleiotropy)2.000000e-10
GCST009541_9Heart failure1.000000e-09
GCST010321_125PR interval3.000000e-19
GCST010796_1565Electrocardiogram morphology (amplitude at temporal datapoints)5.000000e-27
GCST010796_1566Electrocardiogram morphology (amplitude at temporal datapoints)9.000000e-12
GCST010796_1567Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-14
GCST010796_1568Electrocardiogram morphology (amplitude at temporal datapoints)5.000000e-17
GCST010796_1569Electrocardiogram morphology (amplitude at temporal datapoints)5.000000e-19
GCST010796_1570Electrocardiogram morphology (amplitude at temporal datapoints)6.000000e-20
GCST010796_1571Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-20
GCST010796_1572Electrocardiogram morphology (amplitude at temporal datapoints)7.000000e-22
GCST010796_1573Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-22
GCST010796_1574Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-23
GCST010796_1575Electrocardiogram morphology (amplitude at temporal datapoints)8.000000e-25
GCST011205_16Hypertrophic cardiomyopathy (MTAG)5.000000e-11
GCST011211_11Hypertrophic cardiomyopathy3.000000e-11

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0006340mean arterial pressure
EFO:0006335systolic blood pressure
EFO:0004462PR interval
EFO:0004327electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression2
Testosteroneincreases expression, decreases expression, affects cotreatment2
Valproic Acidincreases methylation, increases expression2
aristolochic acid Iincreases expression1
arseniteaffects expression1
CGP 52608increases reaction, affects binding1
abrineincreases expression1
incobotulinumtoxinAdecreases expression1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Calcitriolincreases expression, affects cotreatment1
Doxorubicinaffects expression1
Naledaffects expression1
Progesteroneincreases expression1
Triclosandecreases expression1
Cadmium Chlorideincreases expression1
Copper Sulfateincreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): heart failure