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ACTL9

gene
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Also known as MGC33407

Summary

ACTL9 (actin like 9, HGNC:28494) is a protein-coding gene on chromosome 19p13.2, encoding Actin-like protein 9 (Q8TC94). Testis-specic protein that plays an important role in fusion of proacrosomal vesicles and perinuclear theca formation.

Predicted to be a structural constituent of cytoskeleton. Involved in acrosome assembly and fertilization. Located in acrosomal vesicle; perinuclear theca; and sperm head. Implicated in spermatogenic failure 53.

Source: NCBI Gene 284382 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

  • Gene–disease (curated): spermatogenic failure 53 (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 23
  • Clinical variants (ClinVar): 76 total — 3 pathogenic
  • Phenotypes (HPO): 3
  • Constraint (gnomAD): pLI 0.19 (intermediate), LOEUF 1.57 (unconstrained)
  • MANE Select transcript: NM_178525

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28494
Approved symbolACTL9
Nameactin like 9
Location19p13.2
Locus typegene with protein product
StatusApproved
AliasesMGC33407
Ensembl geneENSG00000181786
Ensembl biotypeprotein_coding
OMIM619251
Entrez284382

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

MANE Select: ENST00000324436

ENST00000324436

RefSeq mRNA: 1 — MANE Select: NM_178525 NM_178525

CCDS: CCDS12207

Canonical transcript exons

ENST00000324436 — 1 exons

ExonStartEnd
ENSE0000122736286974008698795

Expression profiles

Bgee: expression breadth broad, 28 present calls, max score 96.80.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1494 / max 146.6026, expressed in 3 samples.

Highest expression (Bgee): male germ line stem cell (sensu Vertebrata) in testis, sperm, testis, adult organism, quadriceps femoris.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ACTL9 is not an eGene in any GTEx v10 tissue: no tissue shows a variant significantly associated with its expression or splicing (q < 0.05).

FANTOM5 promoters

3 alternative TSS:

Promoter IDTPM avgSamples expressed
1789730.09143
1789720.05113
1789710.00683

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047396.80gold quality
spermCL:000001996.51gold quality
left testisUBERON:000453394.88gold quality
right testisUBERON:000453494.84gold quality
testisUBERON:000047391.73gold quality
adult organismUBERON:000702390.98gold quality
quadriceps femorisUBERON:000137760.42gold quality
vastus lateralisUBERON:000137960.41gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450258.52gold quality
biceps brachiiUBERON:000150757.22gold quality
cardiac muscle of right atriumUBERON:000337954.34gold quality
left ventricle myocardiumUBERON:000656654.23gold quality
kidney epitheliumUBERON:000481953.93gold quality
upper arm skinUBERON:000426353.52gold quality
epithelial cell of pancreasCL:000008353.37gold quality
deltoidUBERON:000147653.18gold quality
tibialis anteriorUBERON:000138553.12silver quality
ileal mucosaUBERON:000033152.70silver quality
myocardiumUBERON:000234950.25gold quality
amniotic fluidUBERON:000017349.55silver quality
pancreatic ductal cellCL:000207949.44silver quality
skeletal muscle tissueUBERON:000113447.83gold quality
nasal cavity epitheliumUBERON:000538447.03gold quality
muscle tissueUBERON:000238546.66gold quality
jejunumUBERON:000211545.69gold quality
cauda epididymisUBERON:000436045.59silver quality
layer of synovial tissueUBERON:000761643.55gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
epithelium of nasopharynxUBERON:000195142.73gold quality
secondary oocyteCL:000065542.57gold quality
substantia nigra pars reticulataUBERON:000196642.38gold quality
upper leg skinUBERON:000426242.01silver quality
buccal mucosa cellCL:000233641.65gold quality
superficial temporal arteryUBERON:000161441.33gold quality
palpebral conjunctivaUBERON:000181241.10gold quality
Brodmann (1909) area 23UBERON:001355441.01gold quality
mucosa of paranasal sinusUBERON:000503040.98gold quality
tongueUBERON:000172340.79gold quality
cartilage tissueUBERON:000241840.77gold quality
jejunal mucosaUBERON:000039940.59gold quality
gingival epitheliumUBERON:000194940.43gold quality
bone marrow cellCL:000209240.34gold quality
germinal epithelium of ovaryUBERON:000130440.33gold quality
esophagus squamous epitheliumUBERON:000692040.29gold quality
epithelium of mammary glandUBERON:000324440.14gold quality
oviduct epitheliumUBERON:000480440.03gold quality
mammary ductUBERON:000176539.98gold quality
mucosa of sigmoid colonUBERON:000499339.95gold quality
saphenous veinUBERON:000731839.83gold quality
parotid glandUBERON:000183139.81gold quality
oocyteCL:000002339.80gold quality
urethraUBERON:000005739.80gold quality
heart right ventricleUBERON:000208039.79gold quality
pericardiumUBERON:000240739.77gold quality
endothelial cellCL:000011539.75gold quality
synovial jointUBERON:000221739.70gold quality
dorsal root ganglionUBERON:000004439.68gold quality
nippleUBERON:000203039.68gold quality
bronchial epithelial cellCL:000232839.65gold quality
deciduaUBERON:000245039.65gold quality
penisUBERON:000098939.64gold quality
gingivaUBERON:000182839.64gold quality
bronchusUBERON:000218539.64gold quality
mammalian vulvaUBERON:000099739.63gold quality
trigeminal ganglionUBERON:000167539.63gold quality
tendon of biceps brachiiUBERON:000818839.60gold quality
inferior vagus X ganglionUBERON:000536339.57gold quality
superior surface of tongueUBERON:000737139.56gold quality
pylorusUBERON:000116639.55gold quality
renal medullaUBERON:000036239.53gold quality
colonic mucosaUBERON:000031739.51gold quality
ponsUBERON:000098839.51gold quality
thymusUBERON:000237039.50gold quality
medulla oblongataUBERON:000189639.48gold quality
superior vestibular nucleusUBERON:000722739.47gold quality
cardia of stomachUBERON:000116239.46gold quality
parietal pleuraUBERON:000240039.45gold quality
dorsal plus ventral thalamusUBERON:000189739.38gold quality
cerebellar vermisUBERON:000472039.37gold quality
oral cavityUBERON:000016739.35gold quality
subthalamic nucleusUBERON:000190639.35gold quality
ventral tegmental areaUBERON:000269139.35gold quality
tracheaUBERON:000312639.33gold quality
parietal lobeUBERON:000187239.32gold quality
vena cavaUBERON:000408739.31gold quality
pharyngeal mucosaUBERON:000035539.27gold quality
substantia nigra pars compactaUBERON:000196539.23gold quality
visceral pleuraUBERON:000240139.23gold quality
postcentral gyrusUBERON:000258139.23gold quality
body of tongueUBERON:001187639.22gold quality
medial globus pallidusUBERON:000247739.18gold quality
trabecular bone tissueUBERON:000248339.18gold quality
globus pallidusUBERON:000187539.15gold quality
entorhinal cortexUBERON:000272839.05gold quality
lateral nuclear group of thalamusUBERON:000273639.00gold quality
corpus epididymisUBERON:000435938.98gold quality
tibiaUBERON:000097938.93gold quality
lateral globus pallidusUBERON:000247638.81gold quality
seminal vesicleUBERON:000099838.75gold quality
caput epididymisUBERON:000435838.75gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.20

HPA expression

RNA tissue specificity: Tissue enriched

2 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPM
Testistissue25.5
Frontal cortextissue0.1

Regulation

Is transcription factor: no

Functional genomics

gnomAD constraint: pLI 0.187, LOEUF 1.57, missense Z -0.551 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000324436 — one region, missense o/e 1.05.

Literature-anchored findings (GeneRIF, showing 4)

  • Association of KIF3A, but not OVOL1 and ACTL9, with atopic eczema in Italian patients (PMID:23278845)
  • KIF3A and OVOL1, but not ACTL9, are involved in the development of Atopic dermatitis in the Chinese pediatric population. (PMID:26127003)
  • Homozygous pathogenic variants in ACTL9 cause fertilization failure and male infertility in humans and mice. (PMID:33626338)
  • Identification of a new mutation in the ACTL9 gene in men with unexplained infertility. (PMID:38769899)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusActl9ENSMUSG00000092519
rattus_norvegicusActl9bENSRNOG00000026033
rattus_norvegicusActl9ENSRNOG00000049571

Paralogs (26): ACTR6 (ENSG00000075089), ACTB (ENSG00000075624), ACTL6B (ENSG00000077080), ACTR5 (ENSG00000101442), ACTR3C (ENSG00000106526), ACTA2 (ENSG00000107796), ACTR8 (ENSG00000113812), ACTR1B (ENSG00000115073), ACTR3 (ENSG00000115091), ACTL8 (ENSG00000117148), ACTRT1 (ENSG00000123165), ACTR10 (ENSG00000131966), ACTR3B (ENSG00000133627), ACTL6A (ENSG00000136518), ACTR2 (ENSG00000138071), ACTR1A (ENSG00000138107), ACTA1 (ENSG00000143632), ACTL7B (ENSG00000148156), ACTC1 (ENSG00000159251), ACTG2 (ENSG00000163017), ACTBL2 (ENSG00000169067), ACTRT2 (ENSG00000169717), ACTG1 (ENSG00000184009), ACTRT3 (ENSG00000184378), ACTL7A (ENSG00000187003), ACTL10 (ENSG00000288649)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1916731) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 6 distinct phenotype terms.

Mouse phenotype (MP)Records
impaired fertilization1
abnormal spermatid morphology1
abnormal acrosome morphology1
detached acrosome1
abnormal acrosome assembly1
abnormal proacrosomal vesicle fusion1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Bos taurusQ2T9W481.0%Diamond
Debaryomyces hansenii CBS767Q6BXN073.9%Diamond
Saccharomyces cerevisiae S288CQ1250963.2%Diamond
Dictyostelium discoideumQ54KZ742.6%Diamond
Schizosaccharomyces pombe 972h-Q9UTQ734.5%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
NFILZprotein-coding105372267
ZNF558protein-coding148156
OR2Z1protein-coding284383
MBD3L1protein-coding85509
MUC16protein-coding94025
MYO1Fprotein-coding4542
ADAMTS10protein-coding81794
ZNF414protein-coding84330

Protein

Protein identifiers

Actin-like protein 9 — Q8TC94 (reviewed: Q8TC94)

All UniProt accessions (1): Q8TC94

UniProt curated annotations — full annotation on UniProt →

Function. Testis-specic protein that plays an important role in fusion of proacrosomal vesicles and perinuclear theca formation.

Subunit / interactions. Interacts with ACTL7A.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Acrosome. Cytoplasm. Cytoskeleton. Perinuclear theca.

Tissue specificity. Testis-specific.

Disease relevance. Spermatogenic failure 53 (SPGF53) [MIM:619258] An autosomal recessive infertility disorder characterized by impaired oocyte fertilization due to oocyte activation failure, in association with structural anomalies in sperm heads. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the actin family.

RefSeq proteins (1): NP_848620* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004000ActinFamily
IPR043129ATPase_NBDHomologous_superfamily

Pfam: PF00022

UniProt features (11 total): sequence variant 8, chain 1, region of interest 1, sequence conflict 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TC94-F187.560.74

Human Protein Atlas

Protein class: Predicted intracellular proteins, Disease related genes, Human disease related genes

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): acrosome; equatorial segment

Antibody reliability (HPA): IH uncertain · IF supported

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 54 (showing top): GOBP_SINGLE_FERTILIZATION, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, GOBP_MALE_GAMETE_GENERATION, GOBP_SECRETORY_GRANULE_ORGANIZATION, GOBP_CELLULAR_COMPONENT_ASSEMBLY_INVOLVED_IN_MORPHOGENESIS, GOBP_ACROSOME_ASSEMBLY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_FERTILIZATION, GOCC_SECRETORY_VESICLE, GOCC_ACROSOMAL_VESICLE, chr19p13

GO Biological Process (4): acrosome assembly (GO:0001675), single fertilization (GO:0007338), fertilization (GO:0009566), cytoskeleton organization (GO:0007010)

GO Molecular Function (2): structural constituent of cytoskeleton (GO:0005200), protein binding (GO:0005515)

GO Cellular Component (5): acrosomal vesicle (GO:0001669), actin cytoskeleton (GO:0015629), perinuclear theca (GO:0033011), sperm head (GO:0061827), cytoplasmic vesicle (GO:0031410)

GO top-level categories

19 GO namespaces:

CategoryTerms
cytoskeleton3
developmental process involved in reproduction1
spermatid development1
cellular component assembly involved in morphogenesis1
cellular process involved in reproduction in multicellular organism1
secretory granule organization1
organelle assembly1
fertilization1
sexual reproduction1
reproductive process1
organelle organization1
structural molecule activity1
cytoskeleton organization1
binding1
secretory granule1
perinuclear region of cytoplasm1
cellular anatomical structure1
cytoplasm1
intracellular vesicle1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 5 of 11 annotations. The rest are phylogenetic / computational / electronic (IEA).

5 experimentally-supported GO terms:

GO termNSEvidence
acrosome assemblyBPmutant phenotype
fertilizationBPdirect assay
acrosomal vesicleCCdirect assay
perinuclear thecaCCdirect assay
sperm headCCdirect assay

Protein interactions and networks

STRING

showing 15 of 1,631 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
ACTL9PLCZ1Q86YW0643
ACTL9OVOL1O14753570
ACTL9TLE6Q9H808551
ACTL9DNAH17Q9UFH2539
ACTL9WEE2P0C1S8531
ACTL9OR2Z1Q8NG97492
ACTL9OR10A3P58181469
ACTL9TMEM232C9JQI7461
ACTL9KIF3AQ9Y496441
ACTL9NLRP5P59047432
ACTL9EMSYQ7Z589430
ACTL9ZGPATQ8N5A5385
ACTL9ROPN1BQ9BZX4360
ACTL9IQCNQ9H0B3359
ACTL9SLC25A46Q96AG3352

IntAct

BioGRID (3 interactions; top human partners by supporting records): CUL3 (Affinity Capture-MS), POLI (Reconstituted Complex), QRICH1 (Two-hybrid)

Disease & clinical

Genetic variants

Variant evidence for ACTL9: 76 ClinVar records (3 pathogenic / likely pathogenic); 23 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic3
Likely pathogenic0
Uncertain significance67
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (3)

Showing all 3 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
1048625NM_178525.5(ACTL9):c.1034C>T (p.Ser345Leu)Pathogenicno assertion criteria provided1
1048626NM_178525.5(ACTL9):c.1138G>T (p.Val380Leu)Pathogenicno assertion criteria provided1
1048627NM_178525.5(ACTL9):c.1209C>G (p.Tyr403Ter)Pathogenicno assertion criteria provided1

Per-variant reference — Sugi Variant

Explore ACTL9’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 19 predictions of 51):

Position(s)EffectΔscoreSites
19:8698178donor_gain0.5200
19:8698174donor_gain0.4000
19:8697714donor_gain0.3600
19:8698072–8698073acceptor_loss0.34006
19:8698074acceptor_loss0.3300
19:8697925donor_gain0.3200
19:8697730donor_gain0.3100
19:8697829donor_gain0.3100
19:8698354acceptor_gain0.2600
19:8698514–8698515donor_loss0.26005

HPA cancer prognostics

RNA cancer specificity: Not detected

Disease associations

OMIM: gene MIM:619251 | disease phenotypes: MIM:619258

GenCC curated gene-disease

2 curated gene-disease records:

DiseaseClassificationInheritanceRecords
spermatogenic failure 53StrongAutosomal recessive2
non-syndromic male infertility due to sperm motility disorderSupportiveAutosomal recessive

Mondo (2): spermatogenic failure 53 (MONDO:0030989), (MONDO:0017173)

HPO phenotypes

3 phenotypes (HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0003251Male infertility
HP:0032562Tapered sperm head

GWAS associations

23 associations:

StudyTraitp-value
GCST008363_8Offspring birth weight2e-25
GCST008363_129Offspring birth weight6e-25
GCST004861_30Itch intensity from mosquito bite4e-15
GCST003184_11Atopic dermatitis5e-12
GCST004862_191Itch intensity from mosquito bite adjusted by bite size8e-12
GCST003184_1Atopic dermatitis2e-11
GCST010984_45Allergic disease (asthma, hay fever and/or eczema) (multivariate analysis)5e-11
GCST010985_49Allergic disease (asthma, hay fever and/or eczema) (age of onset)5e-11
GCST007800_56Asthma (childhood onset)5e-10
GCST003995_5Tonsillectomy1e-9
GCST004865_20Itch intensity from mosquito bite adjusted by bite size1e-9
GCST005014_100Tonsillectomy1e-9
GCST004862_157Itch intensity from mosquito bite adjusted by bite size5e-9
GCST001363_2Atopic dermatitis7e-9
GCST008362_12Birth weight1e-8
GCST008362_124Birth weight1e-8
GCST005146_51Birth weight2e-8
GCST90007329_1circulating leptin levels adjusted for BMI2e-7
GCST90007323_1circulating leptin levels adjusted for BMI4e-7
GCST90007326_1circulating leptin levels adjusted for BMI7e-7
GCST007798_3Asthma9e-7
GCST90007320_1circulating leptin levels adjusted for BMI9e-7
GCST004523_10Resting metabolic rate9e-6

EFO canonical traits (from GWAS)

8 canonical traits:

EFO IDTrait name
EFO:0007924tonsillectomy risk measurement
EFO:0008004resting metabolic rate measurement
EFO:0008377mosquito bite reaction itch intensity measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0004344birth weight
EFO:0005939parental genotype effect measurement
EFO:0004847age at onset
EFO:0007793BMI-adjusted leptin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

ChemicalActions (top 5)PubMed papers
terbufosincreases methylation1
Resveratrolaffects cotreatment, decreases expression1
Benzo(a)pyreneincreases methylation, affects methylation1
Fonofosincreases methylation1
Parathionincreases methylation1
Plant Extractsaffects cotreatment, decreases expression1
Valproic Acidincreases methylation1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

12 trials:

NCTPhaseStatusTitle
NCT03414970Phase 3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344Phase 2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999Phase 2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364Phase 1/2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855Phase 1/2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908Early Phase 1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041Early Phase 1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT07628634Early Phase 1RECRUITINGFeasibility Study on the Effect of a Methionine-Reduced Diet on Serum Levels in Pts w/ Solid Tumors
NCT01208974Not specifiedCOMPLETEDNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery