SPATC1L

gene
On this page

Summary

SPATC1L (spermatogenesis and centriole associated 1 like, HGNC:1298) is a protein-coding gene on chromosome 21q22.3, encoding Speriolin-like protein (Q9H0A9).

Enables identical protein binding activity. Predicted to be involved in spermatogenesis. Predicted to act upstream of or within actin polymerization or depolymerization; positive regulation of cAMP-dependent protein kinase activity; and positive regulation of cAMP/PKA signal transduction. Located in cytoplasm.

Source: NCBI Gene 84221 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): hearing loss disorder (Moderate, GenCC)
  • Clinical variants (ClinVar): 99 total
  • MANE Select transcript: NM_001142854

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1298
Approved symbolSPATC1L
Namespermatogenesis and centriole associated 1 like
Location21q22.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000160284
Ensembl biotypeprotein_coding
OMIM612412
Entrez84221

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000291672, ENST00000330205, ENST00000872417, ENST00000872418, ENST00000872419, ENST00000872420, ENST00000967863, ENST00000967864

RefSeq mRNA: 2 — MANE Select: NM_001142854 NM_001142854, NM_032261

CCDS: CCDS13732, CCDS46653

Canonical transcript exons

ENST00000291672 — 5 exons

ExonStartEnd
ENSE000010511474616191646162067
ENSE000013094484618435646184459
ENSE000021176654616116046161705
ENSE000022812214618262446183774
ENSE000034799134616830846168658

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 92.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.6371 / max 379.7846, expressed in 1702 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
19091324.60321702
1909090.02757
1909080.00642

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453492.73gold quality
left testisUBERON:000453392.02gold quality
testisUBERON:000047391.36gold quality
left adrenal gland cortexUBERON:003582587.35gold quality
prostate glandUBERON:000236786.28gold quality
right adrenal gland cortexUBERON:003582786.21gold quality
putamenUBERON:000187486.20gold quality
temporal lobeUBERON:000187185.92gold quality
amygdalaUBERON:000187685.84gold quality
right adrenal glandUBERON:000123385.10gold quality
nucleus accumbensUBERON:000188285.02gold quality
Ammon’s hornUBERON:000195484.78gold quality
superior frontal gyrusUBERON:000266184.47gold quality
apex of heartUBERON:000209884.43gold quality
caudate nucleusUBERON:000187384.36gold quality
left adrenal glandUBERON:000123483.96gold quality
anterior cingulate cortexUBERON:000983583.55gold quality
hypothalamusUBERON:000189883.53gold quality
right frontal lobeUBERON:000281083.38gold quality
cerebral cortexUBERON:000095683.14gold quality
frontal cortexUBERON:000187083.04gold quality
dorsolateral prefrontal cortexUBERON:000983482.80gold quality
prefrontal cortexUBERON:000045182.79gold quality
brainUBERON:000095582.29gold quality
Brodmann (1909) area 9UBERON:001354082.08gold quality
mucosa of stomachUBERON:000119981.65gold quality
adrenal glandUBERON:000236981.30gold quality
adenohypophysisUBERON:000219681.27gold quality
pituitary glandUBERON:000000781.06gold quality
substantia nigraUBERON:000203880.76gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no2.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting SPATC1L, 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-371499.7170.742671
HSA-MIR-396099.4166.1196
HSA-MIR-519496.7763.911021
HSA-MIR-6738-5P96.3363.61815
HSA-MIR-6734-5P95.7065.56950
HSA-MIR-1914-3P95.0763.37762

Literature-anchored findings (GeneRIF, showing 7)

  • rs1465567 of EGFLAM and rs113710653 of SPATC1L may be susceptibility loci for true aortic aneurysm and rs143881017 of RNASE13 may be such a locus for dissecting aortic aneurysm in Japanese individuals. (PMID:28339009)
  • TNFSF13, SPATC1L, SLC22A25 and SALL4 may thus be novel susceptibility loci for atrial fibrillation in the Japanese population (PMID:28849223)
  • these results implicate the SPATC1L-PKA complex in maintaining the stability of the sperm head-tail junction, thereby revealing a new molecular basis for sperm head-tail integrity. (PMID:30026308)
  • SPATC1L was identified as a candidate gene for early-onset and age-related hearing loss. (PMID:30177775)
  • PTSD is associated with increased DNA methylation across regions of HLA-DPB1 and SPATC1L. (PMID:33152445)
  • Biallelic mutations in spermatogenesis and centriole-associated 1 like (SPATC1L) cause acephalic spermatozoa syndrome and male infertility. (PMID:34213489)
  • Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage. (PMID:37625567)

Cross-species orthologs

1 orthologs

OrganismSymbolGene ID
mus_musculusSpatc1lENSMUSG00000009115

Paralogs (1): SPATC1 (ENSG00000186583)

Protein

Protein identifiers

Speriolin-like proteinQ9H0A9 (reviewed: Q9H0A9)

Alternative names: Spermatogenesis and centriole-associated protein 1-like protein

All UniProt accessions (1): Q9H0A9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Miscellaneous. Highly variable expression among individuals is associated with differential sensitivity to the DNA alkylating agent N-methyl-N’-nitro-N-nitrosoguanidine (MNNG), decreased expression being associated with increased sensitivity.

Similarity. Belongs to the speriolin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H0A9-11yes
Q9H0A9-22

RefSeq proteins (2): NP_001136326, NP_115637 (=MANE)

Domains & families (InterPro)

IDNameType
IPR026715SPATC1Family
IPR029384Speriolin_CDomain
IPR029385Speriolin_NDomain

Pfam: PF15058, PF15059

UniProt features (9 total): region of interest 2, modified residue 2, sequence variant 2, chain 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H0A9-F169.310.38

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 (2): 60, 134

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): GCANCTGNY_MYOD_Q6, GOBP_MALE_GAMETE_GENERATION, CHANDRAN_METASTASIS_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, YGACNNYACAR_UNKNOWN, GOBP_ACTIN_FILAMENT_ORGANIZATION, HEN1_01, GOCC_CENTROSOME, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, CCCNNGGGAR_OLF1_01, chr21q22, E2A_Q2, GOMF_PROTEIN_KINASE_A_REGULATORY_SUBUNIT_BINDING, GOMF_PROTEIN_KINASE_A_BINDING

GO Biological Process (3): spermatogenesis (GO:0007283), actin polymerization or depolymerization (GO:0008154), positive regulation of cAMP/PKA signal transduction (GO:0141163)

GO Molecular Function (3): protein kinase A regulatory subunit binding (GO:0034237), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (3): cytoplasm (GO:0005737), centrosome (GO:0005813), sperm head-tail coupling apparatus (GO:0120212)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
developmental process involved in reproduction1
male gamete generation1
actin filament organization1
cAMP/PKA signal transduction1
regulation of cAMP/PKA signal transduction1
positive regulation of intracellular signal transduction1
protein kinase A binding1
protein binding1
binding1
intracellular anatomical structure1
centriole1
microtubule organizing center1

Protein interactions and networks

STRING

716 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPATC1LPM20D1Q6GTS8626
SPATC1LSPATA6Q9NWH7594
SPATC1LPMFBP1Q8TBY8581
SPATC1LSUN5Q8TC36531
SPATC1LKRTCAP3Q53RY4511
SPATC1LTSGA10Q9BZW7489
SPATC1LC21orf58P58505475
SPATC1LCEP112Q8N8E3449
SPATC1LYBEYP58557447
SPATC1LSEPTIN8Q92599447
SPATC1LMETTL27Q8N6F8446
SPATC1LTEX9Q8N6V9434
SPATC1LHLA-DPA1P01905425
SPATC1LHIVEP3Q5T1R4418
SPATC1LSLC22A25Q6T423417

IntAct

39 interactions, top by confidence:

ABTypeScore
FSD2SPATC1Lpsi-mi:“MI:0915”(physical association)0.600
SPATC1LFSD2psi-mi:“MI:0915”(physical association)0.600
ARL4ASPATC1Lpsi-mi:“MI:0915”(physical association)0.560
TRIM27SPATC1Lpsi-mi:“MI:0915”(physical association)0.560
TCF4SPATC1Lpsi-mi:“MI:0915”(physical association)0.560
SPATC1LIKZF1psi-mi:“MI:0915”(physical association)0.560
SIAH1SPATC1Lpsi-mi:“MI:0915”(physical association)0.560
SPATC1LPHC2psi-mi:“MI:0915”(physical association)0.560
PNMA1SPATC1Lpsi-mi:“MI:0915”(physical association)0.560
SPATC1LLZTS2psi-mi:“MI:0915”(physical association)0.560
SPATC1LARMC7psi-mi:“MI:0915”(physical association)0.560
SPATC1LARL4Apsi-mi:“MI:0915”(physical association)0.560
SPATC1LTCF4psi-mi:“MI:0915”(physical association)0.560
SPATC1LSIAH1psi-mi:“MI:0915”(physical association)0.560
LZTS2SPATC1Lpsi-mi:“MI:0915”(physical association)0.560
SPATC1LTRIM27psi-mi:“MI:0915”(physical association)0.560
IKZF1SPATC1Lpsi-mi:“MI:0915”(physical association)0.560

BioGRID (60): SPATC1L (Two-hybrid), SPATC1L (Two-hybrid), SPATC1L (Two-hybrid), SPATC1L (Two-hybrid), SPATC1L (Two-hybrid), SPATC1L (Two-hybrid), SPATC1L (Two-hybrid), SPATC1L (Two-hybrid), LZTS2 (Two-hybrid), FSD2 (Two-hybrid), SPATC1L (Affinity Capture-MS), SPATC1L (Two-hybrid), SPATC1L (Affinity Capture-MS), SPATC1L (Proximity Label-MS), SPATC1L (Two-hybrid)

ESM2 similar proteins: A0A0D9SF12, A0A1B0GVZ6, A2A8T7, A2A9F4, A4IFR0, A6H7B4, A6NDZ8, A6NE82, A6NI87, A6NJ08, O76081, O93343, P04289, P0DO92, P24097, P27579, P79348, Q0VD86, Q2HR82, Q2KIL8, Q32LN6, Q5BMD4, Q5R5R7, Q67863, Q68FQ8, Q68US1, Q6AY88, Q6PKN7, Q8BG31, Q8BII1, Q8CF25, Q8K2F3, Q8N4L4, Q8NHZ7, Q8TAG6, Q8TDR4, Q8VC23, Q8VHZ9, Q8WUB2, Q8WWY6

Diamond homologs: Q148B6, Q76KD6, Q9D9W0, Q9H0A9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance84
Likely benign5
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

751 predictions. Top by Δscore:

VariantEffectΔscore
21:46162064:ATCT:Aacceptor_gain1.0000
21:46162066:CT:Cacceptor_gain1.0000
21:46162067:TC:Tacceptor_loss1.0000
21:46162068:C:CAacceptor_loss1.0000
21:46162068:C:CCacceptor_gain1.0000
21:46162063:GATCT:Gacceptor_gain0.9900
21:46162064:ATCTC:Aacceptor_gain0.9900
21:46162065:TCTC:Tacceptor_gain0.9900
21:46162066:CTCTG:Cacceptor_gain0.9900
21:46168302:CCATA:Cdonor_loss0.9900
21:46168303:CATAC:Cdonor_loss0.9900
21:46168305:TACCA:Tdonor_loss0.9900
21:46168306:A:Cdonor_loss0.9900
21:46168326:T:TAdonor_gain0.9900
21:46168659:C:CCacceptor_gain0.9900
21:46168665:C:CTacceptor_gain0.9900
21:46184351:ATCAC:Adonor_loss0.9900
21:46184352:TCACC:Tdonor_loss0.9900
21:46184353:CACC:Cdonor_loss0.9900
21:46184354:ACCT:Adonor_loss0.9900
21:46161910:GCGCA:Gdonor_loss0.9800
21:46161911:CGCA:Cdonor_loss0.9800
21:46161912:GCACC:Gdonor_loss0.9800
21:46161913:CAC:Cdonor_loss0.9800
21:46161914:ACC:Adonor_loss0.9800
21:46161915:C:Adonor_loss0.9800
21:46168306:A:ACdonor_gain0.9800
21:46168307:C:CCdonor_gain0.9800
21:46168666:G:Tacceptor_gain0.9800
21:46161706:C:CCacceptor_gain0.9700

AlphaMissense

2198 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
21:46162004:A:GL203P1.000
21:46162009:G:CF201L1.000
21:46162009:G:TF201L1.000
21:46162011:A:GF201L1.000
21:46161554:C:TG283E0.999
21:46161949:G:CF221L0.999
21:46161949:G:TF221L0.999
21:46161951:A:GF221L0.999
21:46161976:G:CF212L0.999
21:46161976:G:TF212L0.999
21:46161977:A:GF212S0.999
21:46161978:A:GF212L0.999
21:46161998:C:GR205P0.999
21:46162013:G:TA200D0.999
21:46162019:T:AE198V0.999
21:46162022:C:AG197V0.999
21:46162022:C:TG197D0.999
21:46162023:C:AG197C0.999
21:46162023:C:GG197R0.999
21:46161384:A:GW340R0.998
21:46161384:A:TW340R0.998
21:46161389:A:GF338S0.998
21:46161427:G:CC325W0.998
21:46161569:A:GL278P0.998
21:46161950:A:GF221S0.998
21:46161953:C:AG220V0.998
21:46161953:C:TG220D0.998
21:46161995:C:GR206P0.998
21:46162001:T:AD204V0.998
21:46162001:T:GD204A0.998

dbSNP variants (sampled 300 via entrez): RS1000205608 (21:46178901 A>C,G), RS1000245231 (21:46165936 C>A,T), RS1000907753 (21:46179920 G>C), RS1000946724 (21:46177613 G>A), RS1001003017 (21:46161174 T>G), RS1001026101 (21:46173633 G>A), RS1001111991 (21:46166216 AT>A), RS1001159468 (21:46160970 G>A,C,T), RS1001237002 (21:46180137 C>G,T), RS1001552831 (21:46182788 C>G,T), RS1001573425 (21:46177067 A>G), RS1001665963 (21:46163957 G>A), RS1001673667 (21:46171224 C>T), RS1001697311 (21:46171065 G>A,C), RS1001842723 (21:46164676 C>T)

Disease associations

OMIM: gene MIM:612412 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
hearing loss disorderModerateAutosomal recessive

Mondo (1): hearing loss disorder (MONDO:0005365)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
uranyl acetateaffects expression1
sodium arsenitedecreases expression1
di-n-butylphosphoric acidaffects expression1
NSC 689534affects binding, decreases expression1
(+)-JQ1 compounddecreases expression1
Arsenicalsincreases expression1
Benzo(a)pyreneaffects methylation1
Copperaffects binding, decreases expression1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Silicon Dioxideincreases expression1
Thimerosaldecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Uraniumaffects expression1
Valproic Acidincreases expression1
Aflatoxin B1increases methylation1
Cadmium Chloridedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02832128PHASE2COMPLETEDEvaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire)
NCT04915183PHASE2RECRUITINGAtorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer
NCT05258773PHASE2COMPLETEDEvaluation of the Presence of SENS-401 in the Perilymph
NCT06340633PHASE2RECRUITINGSPI-1005 in Adults Receiving Cochlear Implant
NCT00582946PHASE1COMPLETEDWide-Bandwidth Open Canal Hearing Aid For Better Multitalker Speech Understanding
NCT00584155PHASE1WITHDRAWNProtection From Cisplatin Ototoxicity by Lactated Ringers
NCT01206829PHASE1UNKNOWNHearing Impairment, Cognitive Therapy and Coping
NCT01256229PHASE1COMPLETEDOutcomes In Children With Developmental Delay And Deafness
NCT01343394PHASE1WITHDRAWNSafety of Autologous Human Umbilical Cord Blood Mononuclear Fraction to Treat Acquired Hearing Loss in Children
NCT01452607PHASE1COMPLETEDStudy to Evaluate the Safety and Pharmacokinetics of SPI-1005
NCT02259595PHASE1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT04041440PHASE1COMPLETEDSpeech Recognition Training in Children With Hearing Loss
NCT07218913PHASE1RECRUITINGTesting the Addition of Pedmark to Cisplatin Chemotherapy for Reducing Drug-Induced Ear Damage in Men With Stage II-III Metastatic Testicular Germ Cell Tumors
NCT00486577PHASE2/PHASE3COMPLETEDChronic Electrical Stimulation of the Auditory Cortex for Intractable Tinnitus
NCT00789061PHASE2/PHASE3UNKNOWNApplying Proton Pump Inhibitor to Prevent and Treat Acute Fluctuating Hearing Loss in Patients With SLC26A4 Mutation
NCT01423409PHASE2/PHASE3COMPLETEDMulticenter Trial Assessing an Innovative VAS of Pain Among Deaf People
NCT05786378PHASE2/PHASE3UNKNOWNAssessment of The Efficacy of Intratympanic Platelet Rich Plasma for Treatment of Sensorineural Hearing Loss.
NCT01108601PHASE1/PHASE2UNKNOWNTranstympanic Ringer’s Lactate for the Prevention of Cisplatin Ototoxicity
NCT01621256PHASE1/PHASE2COMPLETEDEfficacy, Safety, and Tolerability of Ancrod in Patients With Sudden Hearing Loss
NCT06370351PHASE1/PHASE2RECRUITINGA Phase I/II Clinical Trial with SENS-501 in Children Suffering from Severe to Profound Hearing Loss Due to Otoferlin (OTOF) Mutations
NCT06545175PHASE1/PHASE2RECRUITINGIntracochlear Application of VSF1.01 for the Reduction of Cochlear Implant Surgery Related Trauma
NCT07304024PHASE1/PHASE2RECRUITINGA Treatment for a Form of Age-Related Central Auditory Processing Disorder Consisting of Clemastine Fumarate Plus Engineered Sound
NCT01109576EARLY_PHASE1COMPLETEDWorkshops for Veterans With Vision and Hearing Loss
  • Associated diseases: hearing loss disorder
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hearing loss disorder