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Atlas / Gene / STPG2

STPG2

gene
On this page

Also known as MGC46496

Summary

STPG2 (sperm tail PG-rich repeat containing 2, HGNC:28712) is a protein-coding gene on chromosome 4q22.3-q23, encoding Sperm-tail PG-rich repeat-containing protein 2 (Q8N412).

At a glance

  • GWAS associations: 64
  • Clinical variants (ClinVar): 102 total
  • MANE Select transcript: NM_174952

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28712
Approved symbolSTPG2
Namesperm tail PG-rich repeat containing 2
Location4q22.3-q23
Locus typegene with protein product
StatusApproved
AliasesMGC46496
Ensembl geneENSG00000163116
Ensembl biotypeprotein_coding
Entrez285555

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000295268, ENST00000506482, ENST00000522676

RefSeq mRNA: 1 — MANE Select: NM_174952 NM_174952

CCDS: CCDS3645

Canonical transcript exons

ENST00000295268 — 11 exons

ExonStartEnd
ENSE000010717859812842898128592
ENSE000010717889814304298143476
ENSE000010717929813434798134459
ENSE000012351839784077397840932
ENSE000012351949794389797944007
ENSE000012352029797228097972440
ENSE000012352099798115997981318
ENSE000012352159810595398106064
ENSE000012352229810919398109305
ENSE000014344739755887297559117
ENSE000036733229771269997712814

Expression profiles

Bgee: expression breadth ubiquitous, 113 present calls, max score 80.97.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2401 / max 48.9909, expressed in 674 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
532130.9129537
532120.3272158

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.97gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099177.55gold quality
buccal mucosa cellCL:000233660.37silver quality
corpus callosumUBERON:000233656.02gold quality
right uterine tubeUBERON:000130253.18gold quality
islet of LangerhansUBERON:000000652.83gold quality
upper leg skinUBERON:000426252.45silver quality
adult mammalian kidneyUBERON:000008251.90gold quality
calcaneal tendonUBERON:000370151.08silver quality
bone marrow cellCL:000209250.51gold quality
adrenal tissueUBERON:001830350.33gold quality
adenohypophysisUBERON:000219650.30gold quality
pituitary glandUBERON:000000750.25gold quality
thyroid glandUBERON:000204650.05gold quality
prefrontal cortexUBERON:000045149.87gold quality
testisUBERON:000047349.78gold quality
metanephros cortexUBERON:001053349.59gold quality
lower esophagus mucosaUBERON:003583449.42gold quality
right lobe of thyroid glandUBERON:000111949.37gold quality
left lobe of thyroid glandUBERON:000112049.26gold quality
pancreasUBERON:000126449.19gold quality
left testisUBERON:000453349.18gold quality
kidneyUBERON:000211348.89gold quality
gall bladderUBERON:000211048.66gold quality
olfactory segment of nasal mucosaUBERON:000538648.53gold quality
C1 segment of cervical spinal cordUBERON:000646948.46gold quality
right testisUBERON:000453448.23gold quality
right lobe of liverUBERON:000111447.93silver quality
body of pancreasUBERON:000115047.80gold quality
cortex of kidneyUBERON:000122547.80gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no5.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting STPG2, 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-366299.9973.825684
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-624-3P98.3767.061067
HSA-MIR-61796.7965.96738
HSA-MIR-382-5P96.7165.90762
HSA-MIR-59296.5967.59817
HSA-MIR-3605-3P82.5760.7898

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriostpg2ENSDARG00000061060
mus_musculusStpg2ENSMUSG00000047940
rattus_norvegicusStpg2ENSRNOG00000023457

Paralogs (5): STPG1 (ENSG00000001460), CIMAP1A (ENSG00000177947), CIMAP1B (ENSG00000177989), CIMAP1D (ENSG00000181781), CIMAP1C (ENSG00000182950)

Protein

Protein identifiers

Sperm-tail PG-rich repeat-containing protein 2 — Q8N412 (reviewed: Q8N412)

All UniProt accessions (2): H0YAZ7, Q8N412

RefSeq proteins (1): NP_777612* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR010736SHIPPO-rptRepeat
IPR051291CIMAPFamily

Pfam: PF07004

UniProt features (16 total): repeat 9, sequence variant 6, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N412-F162.360.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, SCGGAAGY_ELK1_02, EIF4E_UP, RFX7_TARGET_GENES, ZNF423_TARGET_GENES, MIR6505_5P, MIR592, MIR617, LAKE_ADULT_KIDNEY_C12_THICK_ASCENDING_LIMB, DESCARTES_MAIN_FETAL_PDE1C_ACSM3_POSITIVE_CELLS, CUX1_TARGET_GENES, ZNF236_TARGET_GENES, chr4q23

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1146 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STPG2M1APQ8TC57557
STPG2EFCAB10A6NFE3556
STPG2METAP1P53582508
STPG2RAP1GDS1P52306507
STPG2DEFB125Q8N687475
STPG2CFAP206Q8IYR0450
STPG2CCDC169A6NNP5447
STPG2KBTBD12Q3ZCT8446
STPG2PRODH2Q9UF12428
STPG2AK8Q96MA6418
STPG2TSPAN5P62079411
STPG2SRCAPQ6ZRS2402
STPG2FIGNQ5HY92402
STPG2EXD1Q8NHP7391
STPG2TAFA1Q7Z5A9379

IntAct

3 interactions, top by confidence:

ABTypeScore
STPG2TFpsi-mi:“MI:0914”(association)0.530

BioGRID (11): TF (Affinity Capture-MS), TTC5 (Affinity Capture-MS), NYX (Affinity Capture-MS), TF (Affinity Capture-MS), NYX (Affinity Capture-MS), TTC5 (Affinity Capture-MS), TF (Affinity Capture-MS), NYX (Affinity Capture-MS), TTC5 (Affinity Capture-MS), GDA (Affinity Capture-MS), STPG2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1A5R9, A2AVQ5, A2RRW4, A2RSX4, A5WUY6, A9JS51, B0BM24, B0S4Q5, B1H283, D4A039, F1MMV1, Q08BC4, Q0VB26, Q2T9Q3, Q2TA11, Q2TBS4, Q3KQ80, Q3SX64, Q3TZ65, Q3ZCV2, Q4KKZ1, Q4KLY8, Q4R5Y0, Q5PQN4, Q5RAF2, Q5XI56, Q6ZN84, Q810P2, Q8BUG5, Q8C008, Q8C8J0, Q8IXM7, Q8N412, Q8N6G2, Q8N7U6, Q8N801, Q8TCI5, Q8WW14, Q9D067, Q9D131

Diamond homologs: A1A5R9, Q08BC4, Q8C8J0, Q8N412

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance76
Likely benign8
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1223 predictions. Top by Δscore:

VariantEffectΔscore
4:97580141:A:ACdonor_gain0.9900
4:97712813:ACCTG:Aacceptor_loss0.9900
4:97712814:CCTGA:Cacceptor_loss0.9900
4:97712815:C:CAacceptor_loss0.9900
4:97712816:T:Gacceptor_loss0.9900
4:97712694:CAAA:Cdonor_loss0.9800
4:97712695:AAAC:Adonor_loss0.9800
4:97712696:AACC:Adonor_loss0.9800
4:97712697:ACC:Adonor_loss0.9800
4:97712698:C:Gdonor_loss0.9800
4:97712813:ACCT:Aacceptor_gain0.9800
4:97777116:T:Cdonor_gain0.9800
4:97712699:C:Gdonor_loss0.9700
4:97712812:GACCT:Gacceptor_gain0.9700
4:97720752:A:ACdonor_gain0.9700
4:97573346:T:Cdonor_gain0.9600
4:97580145:CA:Cdonor_gain0.9600
4:97712814:CCT:Cacceptor_gain0.9600
4:97712815:C:CCacceptor_gain0.9600
4:97580118:A:ACdonor_gain0.9500
4:97712815:C:Aacceptor_gain0.9200
4:97712811:GGACC:Gacceptor_gain0.9100
4:97726935:T:TCacceptor_gain0.9100
4:97717859:A:Cdonor_gain0.9000
4:97751675:A:Cdonor_gain0.9000
4:97590406:C:CCacceptor_gain0.8900
4:97815028:C:CTdonor_gain0.8900
4:97815047:C:CTdonor_gain0.8900
4:97815048:T:TTdonor_gain0.8900
4:97682249:A:ACdonor_gain0.8800

AlphaMissense

2978 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:97981190:G:CF247L0.949
4:97981190:G:TF247L0.949
4:97981192:A:GF247L0.949
4:98134443:A:CF42L0.949
4:98134443:A:TF42L0.949
4:98134445:A:GF42L0.949
4:97840819:A:CF386L0.942
4:97840819:A:TF386L0.942
4:97840821:A:GF386L0.942
4:97972355:A:CF286L0.936
4:97972355:A:TF286L0.936
4:97972357:A:GF286L0.936
4:98109264:A:CF143L0.930
4:98109264:A:TF143L0.930
4:98109266:A:GF143L0.930
4:97840813:A:CS388R0.921
4:97840813:A:TS388R0.921
4:97840815:T:GS388R0.921
4:97981211:A:CF240L0.913
4:97981211:A:TF240L0.913
4:97981213:A:GF240L0.913
4:98128453:C:TG121D0.905
4:98128517:A:CY100D0.902
4:97840849:A:CS376R0.901
4:97840849:A:TS376R0.901
4:97840851:T:GS376R0.901
4:98143132:G:TR7S0.893
4:98128454:C:GG121R0.885
4:98143140:C:GR4P0.885
4:98109275:C:GG140R0.875

dbSNP variants (sampled 300 via entrez): RS1000000990 (4:98120762 T>C), RS1000012789 (4:97898847 A>C), RS1000016655 (4:97523287 A>T), RS1000016974 (4:97497519 T>C), RS1000018908 (4:97922170 C>T), RS1000024927 (4:98035939 C>T), RS1000030488 (4:98120980 C>A,T), RS1000034127 (4:97711439 C>G), RS1000036110 (4:97891080 GAGAAC>G), RS1000040190 (4:98122186 T>C,G), RS1000044967 (4:97708370 A>C,G,T), RS1000044984 (4:97576979 C>T), RS1000053380 (4:97872735 C>T), RS1000056527 (4:97639385 C>T), RS1000057254 (4:97751916 C>T)

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

64 associations (top):

StudyTraitp-value
GCST002157_3Response to mTOR inhibitor (everolimus)4.000000e-06
GCST003264_1025Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_1039Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_1041Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_1044Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_1048Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_1049Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_1067Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_1068Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_1089Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_1090Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_1094Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_1099Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_1103Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_1106Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_143Post bronchodilator FEV1/FVC ratio2.000000e-06
GCST003264_151Post bronchodilator FEV1/FVC ratio2.000000e-06
GCST003264_153Post bronchodilator FEV1/FVC ratio2.000000e-06
GCST003264_231Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_233Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_244Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_252Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_263Post bronchodilator FEV1/FVC ratio5.000000e-06
GCST003264_266Post bronchodilator FEV1/FVC ratio5.000000e-06
GCST003264_268Post bronchodilator FEV1/FVC ratio5.000000e-06
GCST003264_294Post bronchodilator FEV1/FVC ratio4.000000e-06
GCST003264_453Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_464Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_469Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST003264_492Post bronchodilator FEV1/FVC ratio3.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0005417response to mTOR inhibitor
EFO:0004713FEV/FVC ratio
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008579risk-taking behaviour
EFO:0010093bitter non-alcoholic beverage consumption measurement
EFO:0006882suicide behaviour measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

ChemicalActions (top 5)PubMed papers
methyleugenoldecreases expression1
bisphenol Aincreases methylation, affects cotreatment1
aflatoxin B2decreases methylation1
Fulvestrantaffects cotreatment, increases methylation1
Benzo(a)pyrenedecreases expression1
Leaddecreases expression1
Tobacco Smoke Pollutionincreases methylation1
Okadaic Aciddecreases expression1

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 73

This page pulls from 73 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot