◎ Sugi Atlas

Atlas / Gene / STK31

STK31

gene
On this page

Also known as TDRD8SgK396

Summary

STK31 (serine/threonine kinase 31, HGNC:11407) is a protein-coding gene on chromosome 7p15.3, encoding Serine/threonine-protein kinase 31 (Q9BXU1).

This gene is similar to a mouse gene that encodes a putative protein kinase with a tudor domain, and shows testis-specific expression. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 56164 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 156 total
  • Druggable target: yes
  • MANE Select transcript: NM_031414

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11407
Approved symbolSTK31
Nameserine/threonine kinase 31
Location7p15.3
Locus typegene with protein product
StatusApproved
AliasesTDRD8, SgK396
Ensembl geneENSG00000196335
Ensembl biotypeprotein_coding
OMIM605790
Entrez56164

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000354639, ENST00000355870, ENST00000405627, ENST00000422637, ENST00000433467, ENST00000444333, ENST00000456014, ENST00000461866, ENST00000476399, ENST00000478321, ENST00000528479, ENST00000529549, ENST00000531170

RefSeq mRNA: 4 — MANE Select: NM_031414 NM_001260504, NM_001260505, NM_031414, NM_032944

CCDS: CCDS43556, CCDS5386, CCDS59049

Canonical transcript exons

ENST00000355870 — 24 exons

ExonStartEnd
ENSE000018518032371021923710335
ENSE000034591072378141923781520
ENSE000034639692379082423790946
ENSE000034767442371223423712286
ENSE000034927102371209923712145
ENSE000035195732378683823786924
ENSE000035195882376964023769756
ENSE000035335122376899523769174
ENSE000035438262378650823786633
ENSE000035455952378547823785603
ENSE000035547412373553823735896
ENSE000035726852372724123727315
ENSE000035744112375271723752832
ENSE000035796822383213623832513
ENSE000036068212375431523754474
ENSE000036188742378798023788129
ENSE000036392082376280123762923
ENSE000036448852377214723772278
ENSE000036538702372909123729249
ENSE000036624422373690423737078
ENSE000036635302381514423815212
ENSE000036674952377100523771124
ENSE000036714592378358323783663
ENSE000036773632371748123717579

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 97.47.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2748 / max 119.0864, expressed in 13 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
776850.075611
776840.068110
776830.05329
776870.04127
776860.01676
2043860.00944
2043850.00666
776880.00393

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047397.47gold quality
right testisUBERON:000453495.15gold quality
left testisUBERON:000453394.66gold quality
testisUBERON:000047393.90gold quality
secondary oocyteCL:000065592.35gold quality
germinal epithelium of ovaryUBERON:000130490.36gold quality
oocyteCL:000002389.01gold quality
spermCL:000001987.85gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.75gold quality
buccal mucosa cellCL:000233684.67silver quality
adult organismUBERON:000702381.80gold quality
sural nerveUBERON:001548872.55gold quality
pancreatic ductal cellCL:000207967.75silver quality
cerebellar hemisphereUBERON:000224565.80gold quality
cerebellar cortexUBERON:000212965.70gold quality
right hemisphere of cerebellumUBERON:001489065.20gold quality
olfactory segment of nasal mucosaUBERON:000538665.04gold quality
cerebellumUBERON:000203764.57gold quality
Brodmann (1909) area 46UBERON:000648361.10gold quality
putamenUBERON:000187460.87gold quality
calcaneal tendonUBERON:000370159.41gold quality
caudate nucleusUBERON:000187358.02gold quality
body of pancreasUBERON:000115057.69gold quality
tibial nerveUBERON:000132357.35gold quality
epithelial cell of pancreasCL:000008357.33gold quality
body of stomachUBERON:000116156.28gold quality
mucosa of stomachUBERON:000119956.24gold quality
duodenumUBERON:000211456.15gold quality
right lungUBERON:000216756.02gold quality
pigmented layer of retinaUBERON:000178255.93gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-134144yes27.48
E-ANND-3yes6.30
E-GEOD-111727no360.61
E-MTAB-8060no48.04
E-MTAB-6075no23.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting STK31, 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-196A-1-3P99.9972.152772
HSA-MIR-589-3P99.9169.622088
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-561-3P99.6470.903647
HSA-MIR-3140-5P99.3969.041136
HSA-MIR-4777-5P99.3367.531148
HSA-MIR-223-5P99.2468.821206
HSA-MIR-3145-3P98.8569.072031
HSA-MIR-4772-3P98.0465.601203

Literature-anchored findings (GeneRIF, showing 10)

  • High STK31 expression is associated with colon cancer. (PMID:22828137)
  • the aberrant expression of STK31 contributes to tumorigenicity in somatic cancer cells (PMID:24667656)
  • The human papillomavirus type 16 oncogene E7 may affect STK31 expression through a DNA methylation-mediated mechanism. (PMID:27044426)
  • Relative STK31 expression level was significantly higher in patients with lymph node metastasis. STK31 expression levels in primary tumorous tissues of metastatic patients were significantly higher than in ANCTs and in lymph nodes samples, both at the RNA level and the protein level. (PMID:28412729)
  • Study demonstrates that, except the testes, STK31 is not expressed in normal tissues but aberrantly expressed in pancreatic cancer (PC) tissues, indicating that STK31 is a cancer-testis (CT) gene in PC. STK31 is reactivated by demethylation and, significantly higher in relapsed patients, or patients with advanced pathologic stage or poorer prognosis, suggesting that STK31 might be of potential clinical value. (PMID:28422722)
  • FBLN1 and STK31 can be possible screening and differentiating biomarkers of colorectal cancer (PMID:29715435)
  • STK31 regulates the proliferation and cell cycle of lung cancer cells via the Wnt/betacatenin pathway and feedback regulation by cmyc. (PMID:31894338)
  • Higher miR-543 levels correlate with lower STK31 expression and longer pancreatic cancer survival. (PMID:33128354)
  • STK31 upregulation is associated with chromatin remodeling in gastric cancer and induction of tumorigenicity in a xenograft mouse model. (PMID:33649810)
  • Spastic Paraplegia 20 and Serine/Threonine Protein Kinase 31 Expression for the Detection of Colorectal Cancer. (PMID:35389570)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriostk31ENSDARG00000056339
mus_musculusStk31ENSMUSG00000023403
rattus_norvegicusStk31ENSRNOG00000057554

Paralogs (1): SND1 (ENSG00000197157)

Protein

Protein identifiers

Serine/threonine-protein kinase 31 — Q9BXU1 (reviewed: Q9BXU1)

Alternative names: Serine/threonine-protein kinase NYD-SPK, Sugen kinase 396

All UniProt accessions (7): A0A140VKG1, A0AAQ5BI58, C9JPB1, C9JQW5, Q9BXU1, E9PRQ0, F8W6E7

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Testis specific.

Similarity. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9BXU1-11yes
Q9BXU1-22
Q9BXU1-33

RefSeq proteins (4): NP_001247433, NP_001247434, NP_113602, NP_116562 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000719Prot_kinase_domDomain
IPR002999TudorDomain
IPR011009Kinase-like_dom_sfHomologous_superfamily
IPR035437SNase_OB-fold_sfHomologous_superfamily
IPR047383Tudor_TDRD8Domain
IPR052451Ser/Thr_kinase-likeFamily

Pfam: PF00069, PF00567

Enzyme classification (BRENDA):

  • EC 2.7.11.1 — non-specific serine/threonine protein kinase (BRENDA: 71 organisms, 682 substrates, 228 inhibitors, 23 Km, 6 kcat entries)

Substrate kinetics (BRENDA)

8 substrates with measured Km, best-characterized 8. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
ATP0.0007–0.6411
KKRAARATSNVFA0.013–0.0453
PAH1 PHOSPHATIDATE PHOSPHATASE0.00022
RRRLSSLRA0.0036–0.00372
GTP0.461
KKRAARASSNVFA0.021
LYS-LYS-PHE-ASN-ARG-THR-LEU-SER-VAL-ALA0.00931
MYELIN BASIC PROTEIN0.1451

Catalyzed reactions (Rhea), 2 shown:

  • L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) (RHEA:17989)
  • L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H(+) (RHEA:46608)

UniProt features (37 total): sequence variant 20, sequence conflict 9, domain 2, binding site 2, splice variant 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BXU1-F176.830.29

Functional residue map

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

Ligand- & substrate-binding residues (2): 716–724; 737

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, GOCC_SECRETORY_GRANULE, GOMF_NUCLEASE_ACTIVITY, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, YOKOE_CANCER_TESTIS_ANTIGENS, GOMF_RNA_ENDONUCLEASE_ACTIVITY, MODULE_171, WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN, GOCC_SECRETORY_VESICLE, GOCC_ACROSOMAL_VESICLE, WEBER_METHYLATED_HCP_IN_SPERM_DN, GOMF_PROTEIN_KINASE_ACTIVITY, GOMF_KINASE_ACTIVITY, VECCHI_GASTRIC_CANCER_EARLY_UP

GO Biological Process (1): protein phosphorylation (GO:0006468)

GO Molecular Function (7): protein serine/threonine kinase activity (GO:0004674), ATP binding (GO:0005524), protein serine kinase activity (GO:0106310), nucleotide binding (GO:0000166), protein kinase activity (GO:0004672), kinase activity (GO:0016301), transferase activity (GO:0016740)

GO Cellular Component (2): acrosomal vesicle (GO:0001669), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein kinase activity2
phosphorylation1
protein modification process1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
kinase activity1
phosphotransferase activity, alcohol group as acceptor1
catalytic activity, acting on a protein1
transferase activity, transferring phosphorus-containing groups1
catalytic activity1
secretory granule1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

734 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STK31PIWIL1Q96J94758
STK31TDRD9Q8NDG6726
STK31PIWIL2Q8TC59651
STK31TDRD5Q8NAT2624
STK31TDRD1Q9BXT4613
STK31RNF17Q9BXT8613
STK31TDRKHQ9Y2W6602
STK31FAM240BA0A1B0GVZ2517
STK31TDRD7Q8NHU6490
STK31AMZ1Q400G9484
STK31CCDC57Q2TAC2462
STK31FASTKD3Q14CZ7460
STK31NKAIN4Q8IVV8446
STK31PCNX1Q96RV3443
STK31DMRT3Q9NQL9438

IntAct

7 interactions, top by confidence:

ABTypeScore
ESR2FBLL1psi-mi:“MI:0914”(association)0.460
STK31VIMpsi-mi:“MI:0915”(physical association)0.400
STK31SEC61Bpsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350

BioGRID (16): STK31 (Biochemical Activity), STK31 (Affinity Capture-MS), STK31 (Biochemical Activity), STK31 (Proximity Label-MS), STK31 (Proximity Label-MS), FAM114A2 (Affinity Capture-MS), HIGD1A (Affinity Capture-MS), FYTTD1 (Affinity Capture-MS), SEC61B (Affinity Capture-MS), STK31 (Affinity Capture-MS), STK31 (Affinity Capture-MS), STK31 (Cross-Linking-MS (XL-MS)), STK31 (Cross-Linking-MS (XL-MS)), STK31 (Cross-Linking-MS (XL-MS)), STK31 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0JM98, A1A5R7, A1L1H3, A5D789, A6NAF9, A9CPT4, B5MCY1, E1BPH3, E1C3S7, E2QTD3, E7FDW8, F1R237, O02671, O60522, O75747, P48357, P61407, Q13075, Q1L981, Q2T9U5, Q460N5, Q4R3G4, Q58EK5, Q5H9U9, Q5M7P8, Q5RE62, Q5SVZ6, Q6NRD5, Q6NU04, Q6YI93, Q6ZSC3, Q86VD1, Q8BGW0, Q8NAT2, Q8NB91, Q8VY10, Q90WE3, Q96C45, Q99MV1, Q99MV7

Diamond homologs: A9CPT4, Q58EK5, Q5REU4, Q66X93, Q78PY7, Q7KZF4, Q7ZT42, Q863B3, Q99MV1, Q99MW1, Q9BXT4, Q9BXU1, Q9FLT0, Q9W0S7, B4QK53, O15530, O55173, O97143, Q6A1A2, Q8FUI5, Q8NU98, Q9M2S4, Q9SZD5, Q9Z2A0, E1BPH3, Q80VL1, Q9Y2W6, D3ZGQ5, Q54VC0, Q86SG6, Q90XC2, Q91ZR4, Q9FL63

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance124
Likely benign19
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3868 predictions. Top by Δscore:

VariantEffectΔscore
7:23712232:A:AGacceptor_gain1.0000
7:23712233:G:GGacceptor_gain1.0000
7:23727240:GATTT:Gacceptor_gain1.0000
7:23727324:T:Gdonor_gain1.0000
7:23727324:T:TGdonor_gain1.0000
7:23727331:T:Gdonor_gain1.0000
7:23729089:A:AGacceptor_gain1.0000
7:23729090:G:GGacceptor_gain1.0000
7:23729229:G:GTdonor_gain1.0000
7:23734286:G:GTdonor_gain1.0000
7:23752709:T:Aacceptor_gain1.0000
7:23752712:TTCA:Tacceptor_loss1.0000
7:23752713:TCA:Tacceptor_loss1.0000
7:23752715:A:AGacceptor_gain1.0000
7:23752716:G:GCacceptor_gain1.0000
7:23752716:GC:Gacceptor_gain1.0000
7:23752716:GCA:Gacceptor_gain1.0000
7:23752716:GCAA:Gacceptor_gain1.0000
7:23752828:ATGAG:Adonor_gain1.0000
7:23752829:TGAG:Tdonor_gain1.0000
7:23752830:GAG:Gdonor_gain1.0000
7:23752830:GAGG:Gdonor_gain1.0000
7:23752833:G:GGdonor_gain1.0000
7:23754297:T:TAacceptor_gain1.0000
7:23754300:T:TAacceptor_gain1.0000
7:23754307:A:AGacceptor_gain1.0000
7:23754308:A:Gacceptor_gain1.0000
7:23754309:A:Gacceptor_gain1.0000
7:23754310:A:Gacceptor_gain1.0000
7:23754310:AATAG:Aacceptor_gain1.0000

AlphaMissense

6775 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:23727282:A:CR97S0.999
7:23727282:A:TR97S0.999
7:23729116:G:TG117V0.999
7:23727281:G:CR97T0.998
7:23729116:G:AG117E0.998
7:23729193:T:GY143D0.998
7:23727280:A:GR97G0.997
7:23712276:T:CF47S0.996
7:23712278:T:AW48R0.996
7:23712278:T:CW48R0.996
7:23712281:G:CA49P0.996
7:23712282:C:AA49D0.996
7:23727248:G:AG86D0.996
7:23727274:T:AW95R0.996
7:23727274:T:CW95R0.996
7:23727283:T:CC98R0.996
7:23727285:C:GC98W0.996
7:23729185:C:AA140D0.996
7:23727256:T:CF89L0.995
7:23727258:T:AF89L0.995
7:23727258:T:GF89L0.995
7:23788017:T:CL842P0.995
7:23727244:T:GY85D0.994
7:23727281:G:TR97I0.994
7:23729109:G:CD115H0.994
7:23729115:G:AG117R0.994
7:23729115:G:CG117R0.994
7:23712275:T:CF47L0.993
7:23712277:T:AF47L0.993
7:23712277:T:GF47L0.993

dbSNP variants (sampled 300 via entrez): RS1000017960 (7:23817749 C>G), RS1000056443 (7:23808013 A>G), RS1000059340 (7:23731202 G>A), RS1000070836 (7:23811919 A>G), RS1000152581 (7:23735406 A>C,G), RS1000195040 (7:23830530 TC>T), RS1000196294 (7:23719342 T>C), RS1000199720 (7:23787356 T>C), RS1000226310 (7:23830762 G>A,T), RS1000227174 (7:23758350 T>A,C), RS1000250128 (7:23813756 A>T), RS1000264316 (7:23713466 T>A), RS1000288531 (7:23819543 T>C), RS1000303383 (7:23790829 G>A), RS1000346141 (7:23826469 C>G,T)

Disease associations

OMIM: gene MIM:605790 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST007565_73Morning person2.000000e-18
GCST007576_362Chronotype2.000000e-18
GCST90011892_6Retinitis pigmentosa8.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008328chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6151 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Other-unique family

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
compound 25 [PMID: 17935989]Inhibition5.85pKi

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression2
lasiocarpinedecreases expression1
methyleugenoldecreases expression1
propionaldehydeincreases expression1
bisphenol Adecreases methylation, affects cotreatment1
butyraldehydedecreases expression1
aflatoxin B2decreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
theaflavin-3,3’-digallateaffects expression1
Fulvestrantaffects cotreatment, decreases methylation1
Lipopolysaccharidesaffects response to substance, increases expression1
N-Nitrosopyrrolidinedecreases expression1
Silicon Dioxidedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1
Particulate Matterincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL941810BindingInhibition of STK31Macrocyclic ureas as potent and selective Chk1 inhibitors: an improved synthesis, kinome profiling, structure-activity relationships, and preliminary pharmacokinetics. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 78

This page pulls from 78 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgtopdb_interactiongwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot