TSPYL1

gene
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Summary

TSPYL1 (TSPY like 1, HGNC:12382) is a protein-coding gene on chromosome 6q22.1, encoding Testis-specific Y-encoded-like protein 1 (Q9H0U9).

The protein encoded by this gene is found in the nucleolus and is similar to that of a family of genes on the Y-chromosome. This gene is intronless. Defects in this gene are a cause of sudden infant death with dysgenesis of the testes syndrome (SIDDT).

Source: NCBI Gene 7259 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): sudden infant death-dysgenesis of the testes syndrome (Strong, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 5 total
  • Phenotypes (HPO): 35
  • MANE Select transcript: NM_003309

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12382
Approved symbolTSPYL1
NameTSPY like 1
Location6q22.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000189241
Ensembl biotypeprotein_coding
OMIM604714
Entrez7259

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000368608, ENST00000652202

RefSeq mRNA: 1 — MANE Select: NM_003309 NM_003309

CCDS: CCDS34518

Canonical transcript exons

ENST00000368608 — 1 exons

ExonStartEnd
ENSE00001447547116274858116279930

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 99.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 55.7689 / max 2081.2741, expressed in 1817 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
7525550.15701816
752513.40911177
752540.8750565
752520.6336271
2041700.4102217
752560.2840129

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
germinal epithelium of ovaryUBERON:000130499.28gold quality
lateral nuclear group of thalamusUBERON:000273699.19gold quality
ponsUBERON:000098899.13gold quality
Brodmann (1909) area 23UBERON:001355499.09gold quality
substantia nigra pars compactaUBERON:000196598.92gold quality
seminal vesicleUBERON:000099898.90gold quality
lateral globus pallidusUBERON:000247698.83gold quality
superior vestibular nucleusUBERON:000722798.82gold quality
parietal lobeUBERON:000187298.79gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.79gold quality
adult organismUBERON:000702398.79gold quality
endothelial cellCL:000011598.73gold quality
postcentral gyrusUBERON:000258198.72gold quality
entorhinal cortexUBERON:000272898.55gold quality
mucosa of paranasal sinusUBERON:000503098.54gold quality
orbitofrontal cortexUBERON:000416798.53gold quality
substantia nigra pars reticulataUBERON:000196698.48gold quality
choroid plexus epitheliumUBERON:000391198.38gold quality
blood vessel layerUBERON:000479798.36gold quality
CA1 field of hippocampusUBERON:000388198.29gold quality
superficial temporal arteryUBERON:000161498.26gold quality
palpebral conjunctivaUBERON:000181298.26gold quality
epithelium of nasopharynxUBERON:000195198.19gold quality
renal medullaUBERON:000036298.17gold quality
superior frontal gyrusUBERON:000266198.12gold quality
corpus epididymisUBERON:000435998.01gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.01gold quality
caput epididymisUBERON:000435897.92gold quality
body of tongueUBERON:001187697.91gold quality
penisUBERON:000098997.89gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-HCAD-5yes615.04
E-HCAD-35yes48.22
E-GEOD-81608no3609.47
E-MTAB-6524no118.09
E-ENAD-27no14.77
E-GEOD-83139no10.24
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

149 targeting TSPYL1, 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-3613-3P100.0076.367965
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-4682100.0068.891258
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-186-5P99.9970.833707
HSA-MIR-366299.9973.825684
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-998599.9872.112939
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-314899.9775.066478
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-548AN99.9770.912817
HSA-MIR-590-3P99.9674.346478
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-545-3P99.9570.742783
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-651-3P99.9473.485177
HSA-MIR-539-5P99.9370.302855
HSA-MIR-314399.9371.963104
HSA-MIR-130599.9171.433443
HSA-MIR-589-3P99.9169.622088
HSA-MIR-449399.9066.48977
HSA-MIR-380-3P99.8970.181978
HSA-MIR-345-3P99.8970.231421

Literature-anchored findings (GeneRIF, showing 7)

  • The chromatin remodeling factor TSPYL1 had a very similar pattern of expression with an incremental increase in HPFH and decreased expression in deltabeta-thalassemia. (PMID:16952470)
  • Mutations in TSPYL1 may contribute to anomalies of testicular development/function. (PMID:19463995)
  • Mutations in the TSPYL1 gene do not seem to play a major role in the pathogenesis of idiopathic male infertility, and mutation screening of the TSPYL1 gene can currently not be recommended in routine diagnostics of idiopathic male infertility. (PMID:22137496)
  • Results show that mutations and polymorphisms in the TSPYL1 gene were not associated with sudden infant death syndrome in a cohort of 165 deceased Swiss infants. (PMID:25449952)
  • The expression of spermatogenic phenotypes of TSPY1 defects is independent of variations in TSPYL1 and TSPYL5 in the Han Chinese population. (PMID:28847364)
  • Unravelling the disease mechanism for TSPYL1 deficiency. (PMID:33075815)
  • TSPYL1 as a Critical Regulator of TGFbeta Signaling through Repression of TGFBR1 and TSPYL2. (PMID:38588050)

Cross-species orthologs

10 orthologs

OrganismSymbolGene ID
danio_reriotspyENSDARG00000005015
danio_rerionap1l4aENSDARG00000070560
mus_musculusTspyl1ENSMUSG00000047514
rattus_norvegicusTspyl1ENSRNOG00000000549
drosophila_melanogasterSetFBGN0014879
drosophila_melanogasterNap1FBGN0015268
drosophila_melanogasterCG3708FBGN0040345
drosophila_melanogastermilFBGN0267366
caenorhabditis_elegansWBGENE00005007
caenorhabditis_elegansWBGENE00017075

Paralogs (19): SET (ENSG00000119335), TSPY2 (ENSG00000168757), NAP1L5 (ENSG00000177432), TSPYL6 (ENSG00000178021), TSPYL5 (ENSG00000180543), TSPYL2 (ENSG00000184205), NAP1L3 (ENSG00000186310), NAP1L2 (ENSG00000186462), NAP1L1 (ENSG00000187109), TSPYL4 (ENSG00000187189), NAP1L4 (ENSG00000205531), TSPY3 (ENSG00000228927), TSPY8 (ENSG00000229549), SETSIP (ENSG00000230667), TSPY4 (ENSG00000233803), TSPY10 (ENSG00000236424), TSPY9 (ENSG00000238074), TSPY1 (ENSG00000258992), (ENSG00000293164)

Protein

Protein identifiers

Testis-specific Y-encoded-like protein 1Q9H0U9 (reviewed: Q9H0U9)

All UniProt accessions (1): Q9H0U9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Expressed in testis, ovary, liver, spleen, brain, kidney, prostate, lung, liver, and heart.

Post-translational modifications. Ubiquitinated by the CRL2(APPBP2) complex, which recognizes the Arg-Xaa-Xaa-Gly sequence at the C-terminus, leading to its degradation.

Disease relevance. Sudden infant death with dysgenesis of the testes syndrome (SIDDT) [MIM:608800] Autosomal recessive disorder. Affected infants appear normal at birth, develop signs of visceroautonomic dysfunction early in life, and die before 12 months of age of abrupt cardiorespiratory arrest. Features included bradycardia, hypothermia, severe gastroesophageal reflux, laryngospasm, bronchospasm, and abnormal cardiorespiratory patterns during sleep. Genotypic males with SIDDT had fetal testicular dysgenesis and ambiguous genitalia, with findings such as intraabdominal testes, dysplastic testes, deficient fetal testosterone production, fusion and rugation of the gonadal sac, and partial development of the penile shaft. Female sexual development was normal. Affected infants had an unusual staccato cry, similar to the cry of a goat. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the nucleosome assembly protein (NAP) family.

RefSeq proteins (1): NP_003300* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002164NAPFamily
IPR037231NAP-like_sfHomologous_superfamily

Pfam: PF00956

UniProt features (10 total): sequence variant 3, compositionally biased region 2, sequence conflict 2, chain 1, region of interest 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H0U9-F162.620.34

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 (1): 156

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 221 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, MORF_IL4, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, GOBP_CHROMATIN_REMODELING, MODULE_114, GOMF_CHROMATIN_BINDING, GOCC_NUCLEOLUS, BLALOCK_ALZHEIMERS_DISEASE_DN, GOMF_HISTONE_BINDING, NUYTTEN_NIPP1_TARGETS_DN, MORF_PAX7, MORF_TNFRSF25, chr6q22

GO Biological Process (1): nucleosome assembly (GO:0006334)

GO Molecular Function (3): chromatin binding (GO:0003682), enzyme binding (GO:0019899), histone binding (GO:0042393)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein binding2
cellular anatomical structure2
nuclear lumen2
chromatin organization1
nucleosome organization1
protein-DNA complex assembly1
binding1
chromosome1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1

Protein interactions and networks

STRING

716 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TSPYL1SIRT1Q96EB6456
TSPYL1SCN1BQ07699428
TSPYL1GABRDO14764423
TSPYL1GABRG2P18507408
TSPYL1SCN1AP35498404
TSPYL1NT5DC1Q5TFE4391
TSPYL1TMEM31Q5JXX7377
TSPYL1ADGRA3Q8IWK6368
TSPYL1PCDH18Q9HCL0364
TSPYL1DMRT1Q9Y5R6355
TSPYL1HSD17B3P37058348
TSPYL1TDRPQ86YL5336
TSPYL1ADAD1Q96M93322
TSPYL1MAMLD1Q13495322
TSPYL1SCN2AQ99250318

IntAct

75 interactions, top by confidence:

ABTypeScore
SLX4ERCC1psi-mi:“MI:0914”(association)0.640
TSPYL1PCM1psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
KSR2POLR3Apsi-mi:“MI:0914”(association)0.530
MAGEA4MAGEB16psi-mi:“MI:0914”(association)0.530
TRIM44ODAD3psi-mi:“MI:0914”(association)0.530
RPL18ARRP8psi-mi:“MI:0914”(association)0.530
ZC3H18AQRpsi-mi:“MI:0914”(association)0.530
TSPYL1GPC3psi-mi:“MI:0914”(association)0.530
NPTNTNPO2psi-mi:“MI:0914”(association)0.530
PSME3HTRA2psi-mi:“MI:0914”(association)0.530
CAPN2MYO9Apsi-mi:“MI:0914”(association)0.530
MAGEA4MAGEA8psi-mi:“MI:0914”(association)0.530
KIF20ANEURL4psi-mi:“MI:0914”(association)0.350
SetZKSCAN1psi-mi:“MI:0914”(association)0.350
ZMYND8MTA3psi-mi:“MI:0914”(association)0.350
PCM1SUPT5Hpsi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
PSME3ZNF891psi-mi:“MI:0914”(association)0.350
SETWDR46psi-mi:“MI:0914”(association)0.350
TSPYL1DVL2psi-mi:“MI:0914”(association)0.350
SOX2SEC16Apsi-mi:“MI:0914”(association)0.350

BioGRID (169): TSPYL1 (Affinity Capture-MS), TSPYL1 (Reconstituted Complex), TSPYL1 (Affinity Capture-MS), TSPYL1 (Affinity Capture-MS), TSPYL1 (Affinity Capture-MS), TSPYL1 (Affinity Capture-MS), NAP1L3 (Affinity Capture-MS), TSPYL2 (Affinity Capture-MS), LCA5 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), SIPA1L2 (Affinity Capture-MS), OSBPL3 (Affinity Capture-MS), SPAG5 (Affinity Capture-MS), SNX6 (Affinity Capture-MS), ZNF687 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

Diamond homologs: A0A494C1R9, A2ZX50, A6NKD2, B8AEC1, B8B2R4, B8B4K9, B9FU45, F4JEI8, O19110, O59797, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0DME0, P53997, P78920, Q01105, Q01534, Q0P5N2, Q18240, Q5R5G8, Q5VND6, Q63945, Q69JW2, Q69ZB3, Q70Z17, Q70Z18, Q70Z19, Q7TQI8, Q86VY4, Q8N831, Q8VD63, Q94K07, Q9BE64, Q9CA59, Q9EQU5, Q9H0U9, Q9H2G4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 102 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
Formation of a pool of free 40S subunits813.2×2e-05
Peptide chain elongation713.1×5e-05
Viral mRNA Translation713.1×5e-05
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA712.9×5e-05
Selenocysteine synthesis712.4×6e-05
Eukaryotic Translation Termination712.4×6e-05
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)712.1×6e-05
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA712.1×6e-05

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis615.2×6e-04
cytoplasmic translation714.4×3e-04
translation89.1×6e-04

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance1
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

5 predictions. Top by Δscore:

VariantEffectΔscore
6:116278691:C:Aacceptor_gain0.3600
6:116278684:C:CCacceptor_gain0.2600
6:116279694:A:ACdonor_gain0.2400
6:116278682:G:GAacceptor_gain0.2100
6:116278692:C:Aacceptor_gain0.2000

AlphaMissense

2857 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:116278693:A:GW380R1.000
6:116278693:A:TW380R1.000
6:116278762:A:GW357R1.000
6:116278762:A:TW357R1.000
6:116278817:C:AK338N1.000
6:116278817:C:GK338N1.000
6:116278839:A:GF331S1.000
6:116278996:A:GW279R1.000
6:116278996:A:TW279R1.000
6:116278997:G:CF278L1.000
6:116278997:G:TF278L1.000
6:116278999:A:GF278L1.000
6:116279028:C:AR268M1.000
6:116278620:G:TP404Q0.999
6:116278628:C:AW401C0.999
6:116278628:C:GW401C0.999
6:116278630:A:GW401R0.999
6:116278630:A:TW401R0.999
6:116278632:A:GL400P0.999
6:116278644:A:TI396N0.999
6:116278691:C:AW380C0.999
6:116278691:C:GW380C0.999
6:116278760:C:AW357C0.999
6:116278760:C:GW357C0.999
6:116278819:T:CK338E0.999
6:116278832:G:CN333K0.999
6:116278832:G:TN333K0.999
6:116278833:T:AN333I0.999
6:116278838:G:CF331L0.999
6:116278838:G:TF331L0.999

dbSNP variants (sampled 300 via entrez): RS1000431105 (6:116280433 G>A), RS1000449847 (6:116275220 C>T), RS1000692317 (6:116281526 G>A), RS1001596711 (6:116280022 G>T), RS1001816012 (6:116281186 G>C), RS1001887930 (6:116281456 T>G), RS1002170539 (6:116278219 T>A), RS1002406462 (6:116274541 T>C), RS1002487042 (6:116278457 G>C), RS1002628118 (6:116277943 G>A,C), RS1002742356 (6:116274860 A>C), RS1002894600 (6:116274628 G>C), RS1004713062 (6:116279508 A>G), RS1004723005 (6:116279252 C>G,T), RS1005345588 (6:116276470 A>T)

Disease associations

OMIM: gene MIM:604714 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
sudden infant death-dysgenesis of the testes syndromeStrongAutosomal recessive

Mondo (1): sudden infant death-dysgenesis of the testes syndrome (MONDO:0012124)

Orphanet (0):

HPO phenotypes

35 total (30 of 35 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000028Cryptorchidism
HP:0000033Ambiguous genitalia, male
HP:0000046Small scrotum
HP:0000062Ambiguous genitalia
HP:0000602Ophthalmoplegia
HP:0001265Hyporeflexia
HP:0001308Tongue fasciculations
HP:0001336Myoclonus
HP:0001510Growth delay
HP:0001522Death in infancy
HP:0001608Abnormality of the voice
HP:0001662Bradycardia
HP:0001695Cardiac arrest
HP:0001699Sudden death
HP:0002020Gastroesophageal reflux
HP:0002045Hypothermia
HP:0002104Apnea
HP:0002267Exaggerated startle response
HP:0002793Abnormal pattern of respiration
HP:0003593Infantile onset
HP:0003623Neonatal onset
HP:0006543Cardiorespiratory arrest
HP:0008708Partial development of the penile shaft
HP:0008733Dysplastic testis
HP:0008736Hypoplasia of penis
HP:0008872Feeding difficulties in infancy
HP:0010307Stridor
HP:0010535Sleep apnea
HP:0011675Arrhythmia

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010002_333Refractive error2.000000e-36

MeSH disease descriptors (1)

DescriptorNameTree numbers
C563856Sudden Infant Death with Dysgenesis of the Testes Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs3828743Efficacy3abiraterone;prednisoloneProstatic Neoplasms

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs3828743DSE, TSPYL134.501abiraterone;prednisolone

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Faffects cotreatment, increases expression1
TAK-243increases sumoylation1
sodium arseniteincreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
celastroldecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
chloropicrindecreases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cadmiumincreases abundance, increases expression1
Coumestroldecreases expression, affects cotreatment1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Ribonucleotidesaffects binding1
Thiramdecreases expression1
Tretinoinincreases expression1
Urethaneincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Cadmium Chlorideincreases abundance, increases expression1
Lactic Acidincreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

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