ESPNL

gene
On this page

Also known as FLJ42568

Summary

ESPNL (espin like, HGNC:27937) is a protein-coding gene on chromosome 2q37.3, encoding Espin-like protein (Q6ZVH7). Binds to but does not cross-link actin.

Predicted to enable actin filament binding activity. Predicted to be involved in actin filament bundle assembly and sensory perception of sound. Predicted to be located in stereocilium tip. Predicted to be active in cytoplasm.

Source: NCBI Gene 339768 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 267 total — 1 pathogenic
  • MANE Select transcript: NM_194312

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:27937
Approved symbolESPNL
Nameespin like
Location2q37.3
Locus typegene with protein product
StatusApproved
AliasesFLJ42568
Ensembl geneENSG00000144488
Ensembl biotypeprotein_coding
OMIM619974
Entrez339768

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000343063, ENST00000409169, ENST00000409506, ENST00000423032, ENST00000477241

RefSeq mRNA: 2 — MANE Select: NM_194312 NM_001308370, NM_194312

CCDS: CCDS2525, CCDS77547

Canonical transcript exons

ENST00000343063 — 9 exons

ExonStartEnd
ENSE00001222582238128707238128904
ENSE00001222599238125270238125384
ENSE00001366247238101941238102131
ENSE00001367620238107791238107973
ENSE00001378370238116903238117034
ENSE00001379324238130128238133287
ENSE00001381095238104656238104842
ENSE00001421662238100340238100713
ENSE00003683324238127622238127734

Expression profiles

Bgee: expression breadth ubiquitous, 139 present calls, max score 70.72.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1529 / max 56.7737, expressed in 44 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
263220.061316
263230.045812
263240.029918
263210.01587

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183170.72gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450269.72gold quality
buccal mucosa cellCL:000233668.88gold quality
oocyteCL:000002368.14gold quality
mammary ductUBERON:000176568.09gold quality
right hemisphere of cerebellumUBERON:001489067.82gold quality
cerebellar vermisUBERON:000472067.58gold quality
cartilage tissueUBERON:000241867.29gold quality
cerebellar hemisphereUBERON:000224567.14gold quality
cerebellumUBERON:000203766.99gold quality
cerebellar cortexUBERON:000212966.94gold quality
mucosa of stomachUBERON:000119966.64gold quality
epithelium of nasopharynxUBERON:000195166.61gold quality
secondary oocyteCL:000065566.57gold quality
spermCL:000001966.25gold quality
deciduaUBERON:000245066.24silver quality
nasal cavity epitheliumUBERON:000538466.19gold quality
vena cavaUBERON:000408765.93gold quality
pharyngeal mucosaUBERON:000035565.68gold quality
right ovaryUBERON:000211864.82gold quality
inferior vagus X ganglionUBERON:000536364.73gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451164.69gold quality
nippleUBERON:000203064.63gold quality
synovial jointUBERON:000221764.55gold quality
saphenous veinUBERON:000731864.47gold quality
right lobe of liverUBERON:000111464.44gold quality
amniotic fluidUBERON:000017364.43gold quality
subthalamic nucleusUBERON:000190664.41gold quality
body of tongueUBERON:001187664.35gold quality
pericardiumUBERON:000240764.32gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no2.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting ESPNL, 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-4455100.0065.481587
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-612499.8769.783551
HSA-MIR-76599.8468.242442
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-6752-3P99.7266.711587
HSA-MIR-182799.6368.573265
HSA-MIR-1915-3P99.5866.791988
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-429199.2068.882969
HSA-MIR-427999.1966.702437
HSA-MIR-442699.1766.741949
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-214-3P98.7168.122128
HSA-MIR-76198.7168.072051
HSA-MIR-1227-5P98.6565.321549
HSA-MIR-429098.5165.17907
HSA-MIR-4726-3P98.4963.891385
HSA-MIR-6742-3P97.9564.501490
HSA-MIR-296-5P97.6164.02851
HSA-MIR-6872-3P97.0866.99750
HSA-MIR-3622A-3P97.0666.431000
HSA-MIR-3622B-3P96.8266.36988
HSA-MIR-582-3P96.6967.381019
HSA-MIR-797396.4865.54502

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioespnlaENSDARG00000078211
danio_rerioespnlbENSDARG00000093112
mus_musculusEspnlENSMUSG00000049515
rattus_norvegicusEspnlENSRNOG00000024717
drosophila_melanogasterfFBGN0262111
caenorhabditis_elegansWBGENE00012319

Paralogs (1): ESPN (ENSG00000187017)

Protein

Protein identifiers

Espin-like proteinQ6ZVH7 (reviewed: Q6ZVH7)

All UniProt accessions (2): Q6ZVH7, C9J6L8

UniProt curated annotations — full annotation on UniProt →

Function. Binds to but does not cross-link actin. Required for the formation and maintenance of inner ear hair cell stereocilia and staircase formation. Essential for normal hearing.

Subunit / interactions. Interacts with MYO3A (via C-terminus). Interacts with MYO3B (via C-terminus).

Subcellular location. Cell projection. Stereocilium.

Isoforms (3)

UniProt IDNamesCanonical?
Q6ZVH7-11yes
Q6ZVH7-22
Q6ZVH7-33

RefSeq proteins (2): NP_001295299, NP_919288* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002110Ankyrin_rptRepeat
IPR036770Ankyrin_rpt-contain_sfHomologous_superfamily
IPR052420Espin/Espin-likeFamily

Pfam: PF12796, PF13637

UniProt features (28 total): repeat 9, region of interest 5, sequence variant 5, sequence conflict 3, compositionally biased region 2, splice variant 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6ZVH7-F165.570.32

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-9662360Sensory processing of sound by inner hair cells of the cochlea
R-HSA-9662361Sensory processing of sound by outer hair cells of the cochlea

MSigDB gene sets: 39 (showing top): GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOBP_ACTIN_FILAMENT_ORGANIZATION, RYTTCCTG_ETS2_B, GOBP_SENSORY_PERCEPTION, GOMF_ACTIN_BINDING, GOCC_NEURON_PROJECTION, GOCC_STEREOCILIUM_BUNDLE, GOCC_CLUSTER_OF_ACTIN_BASED_CELL_PROJECTIONS, GOCC_ACTIN_BASED_CELL_PROJECTION, GOMF_CYTOSKELETAL_PROTEIN_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_SUPRAMOLECULAR_FIBER_ORGANIZATION, GOCC_STEREOCILIUM_TIP, GOMF_PROTEIN_CONTAINING_COMPLEX_BINDING

GO Biological Process (2): sensory perception of sound (GO:0007605), actin filament bundle assembly (GO:0051017)

GO Molecular Function (3): actin filament binding (GO:0051015), actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (4): cytoplasm (GO:0005737), stereocilium tip (GO:0032426), stereocilium (GO:0032420), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Sensory processing of sound2

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
sensory perception of mechanical stimulus1
cellular component assembly1
actin filament bundle organization1
actin binding1
protein-containing complex binding1
cytoskeletal protein binding1
binding1
intracellular anatomical structure1
stereocilium1
stereocilium bundle1
neuron projection1
actin-based cell projection1

Protein interactions and networks

STRING

1099 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ESPNLMYO3BQ8WXR4708
ESPNLMYO3AQ8NEV4675
ESPNLEPS8L2Q9H6S3580
ESPNLLRRC30A6NM36573
ESPNLMATCAP1Q68EN5560
ESPNLWHRNQ9P202533
ESPNLKLHL18O94889531
ESPNLMORN4Q8NDC4523
ESPNLMYO15AQ9UKN7512
ESPNLGRXCR1A8MXD5501
ESPNLPLS1Q14651487
ESPNLTMEM266Q2M3C6475
ESPNLEPS8Q12929450
ESPNLFSCN2O14926445
ESPNLEFHBQ8N7U6435

IntAct

11 interactions, top by confidence:

ABTypeScore
SERTAD2ESPNLpsi-mi:“MI:0915”(physical association)0.560
ESPNLPFDN5psi-mi:“MI:0915”(physical association)0.560
LDLRAP1ESPNLpsi-mi:“MI:0915”(physical association)0.560
KLHL22TRAV18psi-mi:“MI:0914”(association)0.350
ESPNLSERTAD2psi-mi:“MI:0915”(physical association)0.000
ESPNLPFDN5psi-mi:“MI:0915”(physical association)0.000
LDLRAP1ESPNLpsi-mi:“MI:0915”(physical association)0.000

BioGRID (6): ESPNL (Two-hybrid), LDLRAP1 (Two-hybrid), SERTAD2 (Two-hybrid), ESPNL (Affinity Capture-MS), ESPNL (Proximity Label-MS), ESPNL (Proximity Label-MS)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A2R8YCJ5, A2A699, A2AEV7, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NL88, A8MVW0, A9JSM3, B2RU40, B8ZZ34, C9JH25, D4A9R4, J3QNX5, P0CG09, P98077, Q0VD38, Q14761, Q17QH7, Q29RK8, Q2KJ18, Q2M3V2, Q3SX20, Q5BJT1, Q5HZJ5, Q5RKR3, Q5T442, Q64697, Q69YZ2, Q6PB97, Q6PCT2, Q6UXK2, Q6ZMQ8, Q6ZVH7, Q6ZW31, Q80XF7, Q8BLS7

Diamond homologs: A0A0R4IQZ2, A2AS55, A4II29, B4E2M5, C7B178, G0LXV8, L7X8P2, L7XCU0, L7XDS4, P0C0T2, P0C550, P0DJE3, P19838, P23631, P39010, Q04749, Q04861, Q0JKV1, Q10728, Q18297, Q28C34, Q337A0, Q38998, Q3SX00, Q3UMT1, Q3UX43, Q499M5, Q4JHE0, Q5H9F3, Q5R8C8, Q5U5A6, Q63369, Q68DC2, Q6FJ70, Q6GQX6, Q6NRD0, Q6NY19, Q6P6B7, Q6P9J5, Q6ZVH7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance244
Likely benign13
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
997810Single allelePathogenic

SpliceAI

1938 predictions. Top by Δscore:

VariantEffectΔscore
2:238104654:A:AGacceptor_gain1.0000
2:238104655:G:GGacceptor_gain1.0000
2:238104655:GCA:Gacceptor_gain1.0000
2:238104838:GGCTG:Gdonor_gain1.0000
2:238104839:GCTG:Gdonor_gain1.0000
2:238104839:GCTGG:Gdonor_gain1.0000
2:238104843:G:GGdonor_gain1.0000
2:238104844:T:Adonor_loss1.0000
2:238116901:A:AGacceptor_gain1.0000
2:238116902:G:GGacceptor_gain1.0000
2:238117031:GCCG:Gdonor_gain1.0000
2:238117032:CCGG:Cdonor_loss1.0000
2:238117035:G:Cdonor_loss1.0000
2:238117035:G:GGdonor_gain1.0000
2:238117036:T:Adonor_loss1.0000
2:238125382:GCC:Gdonor_gain1.0000
2:238125385:G:GGdonor_gain1.0000
2:238128901:CCAG:Cdonor_loss1.0000
2:238128903:AG:Adonor_loss1.0000
2:238128904:GGTAG:Gdonor_loss1.0000
2:238128905:G:GAdonor_loss1.0000
2:238100711:CAGG:Cdonor_loss0.9900
2:238100712:AGGT:Adonor_loss0.9900
2:238100713:GG:Gdonor_loss0.9900
2:238100714:G:Adonor_loss0.9900
2:238102127:GGCAG:Gdonor_gain0.9900
2:238102128:GCAG:Gdonor_gain0.9900
2:238102128:GCAGG:Gdonor_gain0.9900
2:238102130:AGG:Adonor_loss0.9900
2:238102131:GGTA:Gdonor_loss0.9900

AlphaMissense

6426 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:238128836:T:AW449R0.996
2:238128836:T:CW449R0.996
2:238107953:G:CA279P0.993
2:238128838:G:CW449C0.993
2:238128838:G:TW449C0.993
2:238107858:C:AA247D0.991
2:238107939:C:AP274H0.991
2:238107942:T:AL275H0.989
2:238107855:C:AA246E0.987
2:238107939:C:GP274R0.987
2:238107950:G:CA278P0.987
2:238116976:T:CL310P0.987
2:238104805:C:AA212D0.986
2:238107851:T:CF245L0.986
2:238107853:T:AF245L0.986
2:238107853:T:GF245L0.986
2:238131691:T:AW993R0.986
2:238131691:T:CW993R0.986
2:238107891:T:CL258P0.985
2:238104808:C:AA213D0.984
2:238107857:G:CA247P0.984
2:238116978:G:CA311P0.984
2:238131396:G:CW894C0.984
2:238131396:G:TW894C0.984
2:238131412:T:CF900L0.984
2:238131414:C:AF900L0.984
2:238131414:C:GF900L0.984
2:238104705:T:CC179R0.983
2:238104837:T:AW223R0.983
2:238104837:T:CW223R0.983

dbSNP variants (sampled 300 via entrez): RS1000093965 (2:238114893 C>T), RS1000143784 (2:238109979 A>G), RS1000145006 (2:238104718 A>G), RS1000259275 (2:238121211 A>G), RS1000263045 (2:238116214 A>C), RS1000305408 (2:238126907 G>A), RS1000364944 (2:238125959 T>C), RS1000456137 (2:238100913 T>A,C), RS1000572532 (2:238126796 GTGTA>G), RS1000612764 (2:238101114 G>A,C), RS1000727762 (2:238120091 G>A), RS1000805144 (2:238130978 C>A,T), RS1000832228 (2:238124538 T>A), RS1000913488 (2:238111391 T>G), RS1000992560 (2:238120375 C>A)

Disease associations

OMIM: gene MIM:619974 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): intellectual disability (MONDO:0001071)

Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1increases methylation, increases expression3
aristolochic acid Iincreases expression1
bisphenol Aaffects methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
aflatoxin B2increases methylation1
2-palmitoylglycerolincreases expression1
(+)-JQ1 compounddecreases expression1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinoneincreases expression1
Resveratroldecreases expression, affects cotreatment1
Temozolomidedecreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Rotenonedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Valproic Acidincreases methylation1
Cadmium Chloridedecreases expression1
Okadaic Acidincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394Not specifiedUNKNOWNFCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614Not specifiedCOMPLETEDPsychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405Not specifiedCOMPLETEDTMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.