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SPATS1

gene
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Also known as SPATA8FLJ25442SRSP1

Summary

SPATS1 (spermatogenesis associated serine rich 1, HGNC:22957) is a protein-coding gene on chromosome 6p21.1, encoding Spermatogenesis-associated serine-rich protein 1 (Q496A3).

At a glance

  • GWAS associations: 19
  • Clinical variants (ClinVar): 47 total
  • MANE Select transcript: NM_001372081

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:22957
Approved symbolSPATS1
Namespermatogenesis associated serine rich 1
Location6p21.1
Locus typegene with protein product
StatusApproved
AliasesSPATA8, FLJ25442, SRSP1
Ensembl geneENSG00000249481
Ensembl biotypeprotein_coding
Entrez221409

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 nonsense_mediated_decay

ENST00000288390, ENST00000323108, ENST00000506468, ENST00000515220, ENST00000674044, ENST00000859514

RefSeq mRNA: 2 — MANE Select: NM_001372081 NM_001372081, NM_145026

CCDS: CCDS4911

Canonical transcript exons

ENST00000674044 — 9 exons

ExonStartEnd
ENSE000034684334435272644352873
ENSE000035278144436183144361992
ENSE000035355624436044644360570
ENSE000035738364437635844376473
ENSE000036135384437005144370113
ENSE000036266094436837944368499
ENSE000037576354434309644343234
ENSE000038964534434265044342768
ENSE000038972584437703544380179

Expression profiles

Bgee: expression breadth broad, 63 present calls, max score 85.41.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0882 / max 46.9128, expressed in 26 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
680260.057120
680270.03125

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130285.41gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.22gold quality
left testisUBERON:000453384.35gold quality
testisUBERON:000047383.93gold quality
right testisUBERON:000453483.78gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047374.81gold quality
olfactory segment of nasal mucosaUBERON:000538671.88gold quality
islet of LangerhansUBERON:000000659.58gold quality
fallopian tubeUBERON:000388959.12gold quality
hindlimb stylopod muscleUBERON:000425251.78silver quality
cortical plateUBERON:000534350.96gold quality
right lungUBERON:000216747.77gold quality
prefrontal cortexUBERON:000045146.85gold quality
endometriumUBERON:000129546.76gold quality
bone marrow cellCL:000209246.32gold quality
hypothalamusUBERON:000189845.98gold quality
caudate nucleusUBERON:000187345.86gold quality
sural nerveUBERON:001548845.50gold quality
colonic epitheliumUBERON:000039745.47gold quality
temporal lobeUBERON:000187145.17gold quality
Ammon’s hornUBERON:000195445.14gold quality
amygdalaUBERON:000187644.89gold quality
superior frontal gyrusUBERON:000266143.85gold quality
frontal cortexUBERON:000187042.51gold quality
lungUBERON:000204841.97gold quality
cerebral cortexUBERON:000095641.90gold quality
pancreasUBERON:000126441.70gold quality
Brodmann (1909) area 9UBERON:001354041.24gold quality
brainUBERON:000095541.09gold quality
primary visual cortexUBERON:000243641.03silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no2.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting SPATS1, 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-6759-5P99.9966.54785
HSA-MIR-132-3P99.7370.561424
HSA-MIR-212-3P99.7370.651424
HSA-MIR-6757-3P99.6366.881089
HSA-MIR-5589-3P99.2968.301443
HSA-MIR-477398.3567.301710
HSA-MIR-4704-3P98.2869.331300
HSA-MIR-124397.0765.44719
HSA-MIR-6839-5P96.7468.291088
HSA-MIR-378J96.4466.201020
HSA-MIR-429696.3563.551233
HSA-MIR-426596.1864.68557
HSA-MIR-432296.1864.85539
HSA-MIR-1178-5P95.8364.12504
HSA-MIR-6796-5P95.3766.081120
HSA-MIR-990184.8061.8026

Literature-anchored findings (GeneRIF, showing 1)

  • Dishevelled-DEP domain interacting protein is a negative regulator of the canonical Wnt signaling. (PMID:20603214)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusSpats1ENSMUSG00000023935
rattus_norvegicusSpats1ENSRNOG00000019963

Protein

Protein identifiers

Spermatogenesis-associated serine-rich protein 1 — Q496A3 (reviewed: Q496A3)

All UniProt accessions (3): D6RF91, Q496A3, H0Y9A9

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (2)

UniProt IDNamesCanonical?
Q496A3-11yes
Q496A3-22

RefSeq proteins (2): NP_001359010, NP_659463 (=MANE)

Domains & families (InterPro)

IDNameType
IPR029165SASRP1Family

Pfam: PF15160

UniProt features (10 total): compositionally biased region 3, region of interest 2, chain 1, modified residue 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q496A3-F158.120.09

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): 113

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GCANCTGNY_MYOD_Q6, TAL1ALPHAE47_01, GATA1_04, MYB_Q3, MYB_Q5_01, TGGAAA_NFAT_Q4_01, HEB_Q6, MYB_Q6, chr15q26, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MARTENS_TRETINOIN_RESPONSE_UP, GCAAGAC_MIR431, ERR1_Q2

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1

Protein interactions and networks

STRING

454 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPATS1SPATA3Q8NHX4714
SPATS1SPACA4Q8TDM5624
SPATS1CAPN11Q9UMQ6608
SPATS1TMEM225Q6GV28601
SPATS1TMEM270Q6UE05552
SPATS1DRC5Q5JU00551
SPATS1FBXO36Q8NEA4493
SPATS1TMEM151BQ8IW70479
SPATS1GARIN1BQ96KD3477
SPATS1GTSF1LQ9H1H1471
SPATS1DNAJC14Q6Y2X3451
SPATS1NUP210LQ5VU65449
SPATS1UBQLN3Q9H347438
SPATS1PIH1D2Q8WWB5424
SPATS1SPATA16Q9BXB7424

IntAct

84 interactions, top by confidence:

ABTypeScore
SPATS1KCTD9psi-mi:“MI:0915”(physical association)0.560
ZIC1SPATS1psi-mi:“MI:0915”(physical association)0.560
SPATS1CTNNA3psi-mi:“MI:0915”(physical association)0.560
SPATS1MISPpsi-mi:“MI:0915”(physical association)0.560
CASP6SPATS1psi-mi:“MI:0915”(physical association)0.560
SPATS1CHATpsi-mi:“MI:0915”(physical association)0.560
CRYAASPATS1psi-mi:“MI:0915”(physical association)0.560
SPATS1ATN1psi-mi:“MI:0915”(physical association)0.560
SPATS1psi-mi:“MI:0915”(physical association)0.560
SPATS1EIF2S3psi-mi:“MI:0915”(physical association)0.560
SPATS1ERN1psi-mi:“MI:0915”(physical association)0.560
SPATS1FGFR3psi-mi:“MI:0915”(physical association)0.560
SPATS1FKBP1Apsi-mi:“MI:0915”(physical association)0.560
GRIN2CSPATS1psi-mi:“MI:0915”(physical association)0.560
SPATS1GSNpsi-mi:“MI:0915”(physical association)0.560
HSPA2SPATS1psi-mi:“MI:0915”(physical association)0.560
LAMP2SPATS1psi-mi:“MI:0915”(physical association)0.560
NDUFS5SPATS1psi-mi:“MI:0915”(physical association)0.560
SPATS1KLK6psi-mi:“MI:0915”(physical association)0.560
RANSPATS1psi-mi:“MI:0915”(physical association)0.560
SPATS1SARS1psi-mi:“MI:0915”(physical association)0.560
SPATS1OPTNpsi-mi:“MI:0915”(physical association)0.560
SPATS1TOR1AIP1psi-mi:“MI:0915”(physical association)0.560
UBQLN1SPATS1psi-mi:“MI:0915”(physical association)0.560
PRPF40ASPATS1psi-mi:“MI:0915”(physical association)0.560

BioGRID (11): SPATS1 (Two-hybrid), SPATS1 (Two-hybrid), SPATS1 (Two-hybrid), SPATS1 (Two-hybrid), SPATS1 (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), SPATS1 (Two-hybrid), SPATS1 (Two-hybrid), SPG7 (Two-hybrid), SPATS1 (Two-hybrid), SPATS1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVB3, A0A1B0GVH6, A2RRY8, A4IGV6, A6NHR8, B3DHS1, E1B9I5, O74317, O95561, P03319, P03320, P0C9Z5, P0C9Z6, P10260, P36353, P40744, P40745, Q06616, Q09280, Q09424, Q2KIL1, Q2KIR0, Q32KT7, Q32LB6, Q3T028, Q3TTI8, Q496A3, Q5NC83, Q5SQS8, Q5XIU7, Q68FQ8, Q6DFB0, Q6ZNM6, Q6ZV65, Q811V6, Q8IWA6, Q8N9R6, Q8R0E5, Q8TAL5, Q8WTQ4

Diamond homologs: A2RRY8, Q496A3, Q811V6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1995 predictions. Top by Δscore:

VariantEffectΔscore
15:96783570:C:Gdonor_gain1.0000
15:96784151:A:AGacceptor_gain1.0000
15:96784152:G:GAacceptor_gain1.0000
15:96784152:GA:Gacceptor_gain1.0000
15:96784255:GGAAG:Gdonor_gain1.0000
15:96784256:GAAG:Gdonor_gain1.0000
15:96784256:GAAGG:Gdonor_gain1.0000
15:96784258:AG:Adonor_gain1.0000
15:96784259:GG:Gdonor_gain1.0000
15:96784260:G:GCdonor_loss1.0000
15:96784260:G:GGdonor_gain1.0000
15:96784261:T:Gdonor_loss1.0000
15:96784994:A:AGacceptor_gain1.0000
15:96784995:G:GGacceptor_gain1.0000
15:96784995:GA:Gacceptor_gain1.0000
6:44343236:T:Gdonor_gain1.0000
6:44352869:GTAGA:Gdonor_gain1.0000
6:44352872:GA:Gdonor_gain1.0000
6:44352874:G:GGdonor_gain1.0000
6:44360566:GACGA:Gdonor_gain1.0000
6:44360569:GA:Gdonor_gain1.0000
6:44360571:G:GGdonor_gain1.0000
6:44368497:AAT:Adonor_gain1.0000
6:44368498:AT:Adonor_gain1.0000
6:44368500:G:GGdonor_gain1.0000
6:44370049:A:AGacceptor_gain1.0000
6:44370050:G:GGacceptor_gain1.0000
6:44370050:GA:Gacceptor_gain1.0000
6:44370114:G:GGdonor_gain1.0000
15:96783515:G:Tdonor_gain0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000149848 (6:44358026 G>A,C), RS1000170904 (6:44380553 T>C), RS1000174714 (6:44380105 G>A), RS1000260377 (6:44375876 C>T), RS1000345054 (6:44345439 C>T), RS1000365964 (6:44342996 G>A), RS1000446251 (6:44366820 T>C), RS1000523838 (6:44356444 T>G), RS1000531009 (6:44363245 A>G), RS1000817430 (6:44347571 A>G), RS1000862252 (6:44342756 A>C,G), RS1000909897 (6:44378933 G>T), RS1000910661 (6:44347270 T>C), RS1000955066 (6:44343981 T>A), RS1001027223 (6:44353755 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

19 associations (top):

StudyTraitp-value
GCST000253_23Attention deficit hyperactivity disorder and conduct disorder4.000000e-06
GCST001762_426Obesity-related traits7.000000e-06
GCST002463_21Systemic lupus erythematosus1.000000e-08
GCST002652_13Cotinine glucuronidation4.000000e-08
GCST003072_7Cerebrospinal fluid AB1-42 levels4.000000e-08
GCST003123_30Severe influenza A (H1N1) infection4.000000e-12
GCST003991_4Childhood ear infection4.000000e-14
GCST004250_52Alanine aminotransferase (ALT) levels after remission induction therapy in actute lymphoblastic leukemia (ALL)5.000000e-06
GCST004862_118Itch intensity from mosquito bite adjusted by bite size9.000000e-06
GCST005013_42Childhood ear infection3.000000e-14
GCST007325_40General risk tolerance (MTAG)5.000000e-08
GCST007576_208Chronotype8.000000e-09
GCST007576_400Chronotype9.000000e-07
GCST008513_29Health literacy3.000000e-06
GCST009391_1671Metabolite levels7.000000e-06
GCST009391_640Metabolite levels3.000000e-06
GCST012145_7Ferritin levels8.000000e-06
GCST012485_5Cerebral amyloid angiopathy x sex interaction in Alzheimer’s disease3.000000e-06
GCST90000047_258Age at first sexual intercourse8.000000e-10

EFO canonical traits (16, from GWAS)

EFO IDTrait name
EFO:0004620vitamin B12 measurement
EFO:0006508cotinine glucuronidation measurement
EFO:0004670beta-amyloid 1-42 measurement
EFO:1001488influenza A (H1N1)
EFO:0007904susceptibility to childhood ear infection measurement
EFO:0007965response to combination chemotherapy
EFO:0008377mosquito bite reaction itch intensity measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement
EFO:0010104health literacy measurement
EFO:0010470carnosine measurement
EFO:0010504inositol measurement
EFO:0004459ferritin measurement
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

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Resveratrolaffects cotreatment, decreases expression2
Fulvestrantdecreases methylation1
Air Pollutantsincreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cadmiumdecreases expression, increases abundance1
Carbamazepineaffects expression1
Copperaffects cotreatment, decreases expression1
Diethylhexyl Phthalatedecreases expression1
Indomethacindecreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Smokeincreases abundance, increases expression1
Tobacco Smoke Pollutiondecreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Copper Sulfateincreases expression1

Clinical trials (associated diseases)

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

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
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot