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ESPN

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Summary

ESPN (espin, HGNC:13281) is a protein-coding gene on chromosome 1p36.31, encoding Espin (B1AK53). Multifunctional actin-bundling protein.

This gene encodes a multifunctional actin-bundling protein. It plays a major role in regulating the organization, dimensions, dynamics, and signaling capacities of the actin filament-rich, microvillus-type specializations that mediate sensory transduction in various mechanosensory and chemosensory cells. Mutations in this gene are associated with autosomal recessive neurosensory deafness, and autosomal dominant sensorineural deafness without vestibular involvement.

Source: NCBI Gene 83715 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): nonsyndromic genetic hearing loss (Definitive, ClinGen) — +4 more curated relationships
  • GWAS associations: 3
  • Clinical variants (ClinVar): 699 total — 14 pathogenic, 22 likely-pathogenic (top 5% of genes corpus-wide)
  • GTEx eGene: eQTL in 23 tissues, sQTL in 8 (q < 0.05)
  • Phenotypes (HPO): 26
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.31 (unconstrained)
  • MANE Select transcript: NM_031475

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13281
Approved symbolESPN
Nameespin
Location1p36.31
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000187017
Ensembl biotypeprotein_coding
OMIM606351
Entrez83715

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

MANE Select: ENST00000645284

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 4, TSL 3: 4, TSL 5: 6

ENST00000645284, ENST00000418286, ENST00000434576, ENST00000461727, ENST00000468561, ENST00000475228, ENST00000475479, ENST00000477679, ENST00000478323, ENST00000632142, ENST00000632593, ENST00000632803, ENST00000633239, ENST00000633651, ENST00000636330, ENST00000636644

RefSeq mRNA: 3 — MANE Select: NM_031475 NM_001367473, NM_001367474, NM_031475

CCDS: CCDS70

Canonical transcript exons

ENST00000645284 — 13 exons

ExonStartEnd
ENSE0000160795464402546440440
ENSE0000162807564282266428419
ENSE0000165258864444816444682
ENSE0000166398764486416449091
ENSE0000169485764599996460944
ENSE0000172649864409346441065
ENSE0000175038264406266440808
ENSE0000214088164456646445935
ENSE0000354435264516036451748
ENSE0000361012464518336452096
ENSE0000363078464571846457263
ENSE0000368559664573616457372
ENSE0000382559264247766425249

Expression profiles

Bgee: expression breadth ubiquitous, 184 present calls, max score 98.80.

FANTOM5 (CAGE): breadth broad, TPM avg 4.4751 / max 476.3177, expressed in 563 samples.

Highest expression (Bgee): testis, uterine tube, lobe of liver, mucosa of transverse colon, skin of abdomen.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ESPN is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 23 tissues and its splicing (sQTL) in 8 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 31 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Skin Sun Exposed Lower legeqtl9.5e-73-0.471:6433403:T:C
Skin Not Sun Exposed Suprapubiceqtl2.6e-58-0.451:6433403:T:C
Skin Sun Exposed Lower legsqtl4.6e-29-0.941:6448565:A:G
Testissqtl2.2e-26-0.891:6446883:G:C
Skin Not Sun Exposed Suprapubicsqtl2.9e-25-0.931:6449607:T:C
Whole Bloodeqtl2.9e-20+0.821:6429956:G:A
Esophagus Mucosasqtl1.7e-17-0.751:6448062:G:C
Breast Mammary Tissueeqtl6.0e-12+0.521:6426617:C:T
Nerve Tibialsqtl5.8e-09-0.701:6448652:T:C
Esophagus Mucosaeqtl1.2e-06-0.201:6434339:C:T
Liversqtl1.9e-06-1.041:6448565:A:G
Adipose Subcutaneouseqtl7.5e-05+1.081:6461443:G:A
Pituitarysqtl7.7e-05-0.921:6447167:G:C
Pituitaryeqtl5.2e-04+0.291:6427917:G:A
Brain Hypothalamuseqtl2.2e-03+0.581:6398438:C:A
Testiseqtl3.4e-03-0.181:6313638:T:C
Adipose Visceral Omentumeqtl5.5e-03+1.441:6456963:T:G
Vaginaeqtl7.1e-03+1.831:6761125:G:T
Spleeneqtl7.8e-03+0.661:6403417:C:T
Artery Aortaeqtl1.0e-02-0.411:5640194:T:A

FANTOM5 promoters

showing 10 of 17 alternative TSS:

Promoter IDTPM avgSamples expressed
3812.9652363
3850.5012160
3870.163644
3930.143337
3960.117439
3840.110048
3860.096335
3920.082732
3900.075623
3980.069821

Top tissues by expression

showing 100 of 236 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453498.80gold quality
left testisUBERON:000453398.79gold quality
right uterine tubeUBERON:000130297.93gold quality
right lobe of liverUBERON:000111497.27gold quality
mucosa of transverse colonUBERON:000499196.81gold quality
testisUBERON:000047396.23gold quality
skin of abdomenUBERON:000141694.56gold quality
skin of legUBERON:000151193.64gold quality
liverUBERON:000210793.58gold quality
kidney epitheliumUBERON:000481993.52gold quality
ileal mucosaUBERON:000033193.51gold quality
olfactory segment of nasal mucosaUBERON:000538693.35gold quality
adult mammalian kidneyUBERON:000008293.16gold quality
metanephros cortexUBERON:001053392.81gold quality
lower esophagus mucosaUBERON:003583492.75gold quality
upper arm skinUBERON:000426391.79silver quality
zone of skinUBERON:000001491.17gold quality
adenohypophysisUBERON:000219690.38gold quality
pituitary glandUBERON:000000790.06gold quality
jejunal mucosaUBERON:000039989.40gold quality
duodenumUBERON:000211489.32gold quality
esophagus mucosaUBERON:000246989.01gold quality
small intestine Peyer’s patchUBERON:000345488.54gold quality
buccal mucosa cellCL:000233688.36silver quality
small intestineUBERON:000210888.25gold quality
transverse colonUBERON:000115787.23gold quality
kidneyUBERON:000211385.38gold quality
right hemisphere of cerebellumUBERON:001489084.29gold quality
sural nerveUBERON:001548884.26gold quality
metanephrosUBERON:000008183.89gold quality
cortex of kidneyUBERON:000122583.10gold quality
corpus epididymisUBERON:000435982.79gold quality
spermCL:000001982.34silver quality
cerebellar cortexUBERON:000212982.25gold quality
cerebellar hemisphereUBERON:000224582.13gold quality
tendon of biceps brachiiUBERON:000818881.61silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.54gold quality
cerebellumUBERON:000203781.44gold quality
vaginaUBERON:000099681.40gold quality
tibial nerveUBERON:000132381.22gold quality
nasal cavity mucosaUBERON:000182680.81gold quality
jejunumUBERON:000211580.46gold quality
epithelial cell of pancreasCL:000008379.84gold quality
cardiac muscle of right atriumUBERON:000337979.79gold quality
left ventricle myocardiumUBERON:000656679.79gold quality
intestineUBERON:000016079.64gold quality
gingival epitheliumUBERON:000194979.13silver quality
nasal cavity epitheliumUBERON:000538478.84gold quality
bloodUBERON:000017878.76gold quality
caput epididymisUBERON:000435878.19gold quality
cauda epididymisUBERON:000436078.04gold quality
endocervixUBERON:000045877.32gold quality
minor salivary glandUBERON:000183077.23gold quality
colonUBERON:000115577.21gold quality
colonic mucosaUBERON:000031777.19gold quality
large intestineUBERON:000005977.06gold quality
mouth mucosaUBERON:000372976.69gold quality
cerebellar vermisUBERON:000472076.66gold quality
fallopian tubeUBERON:000388976.55gold quality
rectumUBERON:000105276.41gold quality
quadriceps femorisUBERON:000137776.28gold quality
gingivaUBERON:000182876.20silver quality
saliva-secreting glandUBERON:000104475.95gold quality
mucosa of sigmoid colonUBERON:000499375.50gold quality
vastus lateralisUBERON:000137975.15gold quality
mucosa of paranasal sinusUBERON:000503075.03gold quality
bronchial epithelial cellCL:000232874.58gold quality
right adrenal gland cortexUBERON:003582774.32gold quality
bronchusUBERON:000218574.27gold quality
left uterine tubeUBERON:000130374.14gold quality
esophagusUBERON:000104374.08gold quality
bone marrowUBERON:000237174.07gold quality
left adrenal gland cortexUBERON:003582573.59gold quality
upper leg skinUBERON:000426273.52gold quality
adrenal cortexUBERON:000123573.31gold quality
adult organismUBERON:000702373.27gold quality
prostate glandUBERON:000236773.18gold quality
uterine cervixUBERON:000000273.07gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450272.91gold quality
right adrenal glandUBERON:000123372.68gold quality
left adrenal glandUBERON:000123471.88gold quality
vena cavaUBERON:000408771.47gold quality
nippleUBERON:000203071.20silver quality
skin of hipUBERON:000155471.14silver quality
tonsilUBERON:000237270.76gold quality
esophagus squamous epitheliumUBERON:000692070.69silver quality
trabecular bone tissueUBERON:000248370.42silver quality
pancreatic ductal cellCL:000207970.21silver quality
biceps brachiiUBERON:000150770.14gold quality
ectocervixUBERON:001224969.99gold quality
thymusUBERON:000237069.86silver quality
medial globus pallidusUBERON:000247769.80gold quality
cartilage tissueUBERON:000241869.76gold quality
body of tongueUBERON:001187669.52silver quality
globus pallidusUBERON:000187569.33gold quality
monocyteCL:000057669.30gold quality
adrenal glandUBERON:000236969.24gold quality
oviduct epitheliumUBERON:000480469.13gold quality
saphenous veinUBERON:000731868.87gold quality
secondary oocyteCL:000065568.86silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-125970yes64.56
E-CURD-114yes11.36
E-ANND-3yes3.41

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 75 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Retinatissue109.8
Skin 1tissue87.0not detected
Duodenumtissue85.6high
Small intestinetissue84.5high
Livertissue79.1medium
Testistissue67.2high
Pituitary glandtissue44.8
Epididymistissue38.0high
Kidneytissue35.1high
Cervixtissue28.4medium
Bone marrowtissue26.4not detected
Parathyroid glandtissue25.3
Colontissue23.1high
Vaginatissue21.9not detected
Fallopian tubetissue14.8low
Esophagustissue11.1medium
Salivary glandtissue8.8not detected
Rectumtissue6.4high
Seminal vesicletissue5.8not detected
Prostatetissue4.1not detected
Cerebellumtissue4.0medium
Breasttissue3.8not detected
Adrenal glandtissue3.1medium
Nucleus accumbenstissue2.9
Stomach 1tissue2.5medium
Appendixtissue2.5medium
Endometrium 1tissue2.2not detected
Locus coeruleustissue1.9
Spinal cordtissue1.8
Lungtissue1.7not detected
Hippocampustissue1.5low
Thymustissue1.5
Tonsiltissue1.5not detected
Choroid plexustissue1.4
Medulla oblongatatissue1.4
Pancreastissue1.1not detected
Superior colliculitissue1.0
Frontal cortextissue0.9
Placentatissue0.9low
Postcentral gyrustissue0.9
Skeletal muscletissue0.8not detected
Smooth muscletissue0.8not detected
Midbraintissue0.8
Adipose tissuetissue0.6not detected
Hypothalamustissue0.6
Periaqueductal graytissue0.5
Olfactory bulbtissue0.5
Cerebral cortextissue0.4medium
Urinary bladdertissue0.4medium
Thalamustissue0.4
Spleentissue0.4not detected
Somatosensory cortextissue0.4
Occipital cortextissue0.4
Motor cortextissue0.3
Gallbladdertissue0.3not detected
Hippocampal formationtissue0.3
Entorhinal cortextissue0.3
Temporal cortextissue0.3
Lymph nodetissue0.2not detected
Prefrontal cortextissue0.2

Brain sub-regions (HPA Brain Atlas): detected in 190; highest nTPM — Cerebellar cortex (29.5), Flocculonodular lobe (26.1), Vermis (25.0), Nucleus rhomboideus (13.4), Habenula (6.6).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting ESPN by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 59 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-4283100.0066.422097
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-185-3P99.9567.011743
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-449299.8768.253611
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-76299.5866.611994
HSA-MIR-449899.4767.422360
HSA-MIR-450599.2767.812678
HSA-MIR-3064-5P99.2666.131497
HSA-MIR-3085-3P99.2666.161490
HSA-MIR-6504-5P99.2665.951487
HSA-MIR-578799.2267.862628
HSA-MIR-429199.2068.882969

Functional genomics

gnomAD constraint: pLI 7.27e-24, LOEUF 1.31, missense Z -1.09 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000645284 splits into 3 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
1:6,424,956–6,445,786556 / 633.60.88no
1:6,445,787–6,448,933130 / 223.90.58no
1:6,448,934–6,460,143374 / 381.40.98no

Literature-anchored findings (GeneRIF, showing 11)

  • human deafness and vestibular dysfunction co-segregated with either of two frameshift mutations in ESPN. (PMID:15286153)
  • The results further strengthen the causative role of the espin gene in non-syndromic hearing loss and add new insights into espin structure and function. (PMID:15930085)
  • Here, we report a new activity of the espins, one that depends on their enigmatic WH2 domain: the ability to assemble a large actin bundle when targeted to a specific subcellular location. (PMID:16569662)
  • A recessive ESPN mutation causing congenital hearing loss in a Morocan family was reported. (PMID:18973245)
  • Flies with mutations affecting the diaphanous,forked, and CG12026/TMHS genes displayed significant reductions in the amplitude of sound-evoked potentials compared to wild-type flies (PMID:19102128)
  • The espin actin-filament-binding site has a major effect on the formation and dynamics of actin bundles. (PMID:24424026)
  • The structures of Myo3 in complex with Espin1 not only elucidate the mechanism of the binding, but also reveal a Myo3-induced release of Espin1 auto-inhibition mechanism. (PMID:26785147)
  • The utricles were then treated with a gamma-secretase inhibitor, followed by espin or control transduction and histochemistry. Although gamma-secretase inhibition increased the number of HCs, few had stereociliary arrays. In contrast, 46 h after espin1 transduction, a significant increase in hair-bundle-like structures was observed (PMID:26886463)
  • A significant inverse correlation was observed between miR-612 and Espin protein expression in melanoma tissues. (PMID:29385671)
  • ur study uncovers an additional USH gene, assigns the USH1 phenotype to a variant of ESPN and provides a 12th molecular component to the USH proteome (PMID:29572253)
  • whirlin-espin interaction is important for the architecture of the USH2 complex and actin bundles cross-linked by espin. Our demonstration of whirlin N-terminal fragment interaction with espin, is significantly novel, providing insight into how these two proteins interact to form the USH2 complex. (PMID:31638198)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioespnENSDARG00000076414
mus_musculusEspnENSMUSG00000028943
rattus_norvegicusEspnENSRNOG00000010270
drosophila_melanogasterfFBGN0262111
caenorhabditis_elegansWBGENE00012319

Paralogs (1): ESPNL (ENSG00000144488)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1861630) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 56 distinct phenotype terms.

Mouse phenotype (MP)Records
abnormal organ of Corti morphology2
deafness2
head shaking2
abnormal tectorial membrane morphology2
cochlear hair cell degeneration2
cochlear inner hair cell degeneration2
cochlear outer hair cell degeneration2
pillar cell degeneration2
increased or absent threshold for auditory brainstem response2
abnormal inner ear morphology1
abnormal inner ear vestibule morphology1
organ of Corti degeneration1
abnormal stria vascularis morphology1
tremors1
abnormal nursing1
abnormal stationary movement1
abnormal locomotor behavior1
circling1
bidirectional circling1
abnormal gait1
decreased grooming behavior1
impaired swimming1
impaired balance1
abnormal reflex1
abnormal cochlear hair cell morphology1

+31 more (showing top 25).

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
ACOT7protein-coding11332
HES2protein-coding54626
PLEKHG5protein-coding57449
TNFRSF25protein-coding8718
ZBTB48protein-coding3104
NOL9protein-coding79707
TAS1R1protein-coding80835
MIR4252ncRNA100422975
GPR153protein-coding387509
HES3protein-coding390992

Protein

Protein identifiers

Espin — B1AK53 (reviewed: B1AK53)

Alternative names: Autosomal recessive deafness type 36 protein, Ectoplasmic specialization protein

All UniProt accessions (12): A0A0J9YW00, A0A0J9YWQ8, A0A0J9YY76, A0A1B0GUN9, A0A1B0GUS9, A0A2R8Y6D3, A0A2R8Y7L7, A0A2R8YG57, B1AK53, H0Y7L4, K7EMB7, Q5JYL1

UniProt curated annotations — full annotation on UniProt →

Function. Multifunctional actin-bundling protein. Plays a major role in regulating the organization, dimension, dynamics and signaling capacities of the actin filament-rich microvilli in the mechanosensory and chemosensory cells. Required for the assembly and stabilization of the stereociliary parallel actin bundles. Plays a crucial role in the formation and maintenance of inner ear hair cell stereocilia. Involved in the elongation of actin in stereocilia. In extrastriolar hair cells, required for targeting MYO3B to stereocilia tips, and for regulation of stereocilia diameter and staircase formation.

Subunit / interactions. Monomer. Binds F-actin in a Ca(2+)-resistant fashion. Interacts (via N-terminus) with BAIAP2 (via SH3-domain). Interacts with PFN2. Interacts with MYO3A (via C-terminus). Interacts with MYO3B (via C-terminus).

Subcellular location. Cytoplasm. Cytoskeleton. Cell projection. Stereocilium. Microvillus.

Disease relevance. Deafness, autosomal recessive, 36, with or without vestibular involvement (DFNB36) [MIM:609006] A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNB36 is characterized by prelingual, profound hearing loss, and vestibular areflexia in some patients. The disease is caused by variants affecting the gene represented in this entry. Usher syndrome 1M (USH1M) [MIM:618632] A form of Usher syndrome, a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH1M is an autosomal recessive disease characterized by prelingual sensorineural hearing loss, vestibular dysfunction, night blindness, and progressive impairment of vision. The disease may be caused by variants affecting the gene represented in this entry.

Domain organisation. The WH2-domain binds actin monomer and mediates actin bundle assembly.

Isoforms (2)

UniProt IDNamesCanonical?
B1AK53-11yes
B1AK53-22

RefSeq proteins (3): NP_001354402, NP_001354403, NP_113663* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002110Ankyrin_rptRepeat
IPR003124WH2_domDomain
IPR036770Ankyrin_rpt-contain_sfHomologous_superfamily
IPR052420Espin/Espin-likeFamily

Pfam: PF02205, PF12796, PF13637

UniProt features (49 total): compositionally biased region 10, repeat 9, sequence variant 8, modified residue 6, region of interest 5, sequence conflict 4, splice variant 2, mutagenesis site 2, chain 1, domain 1, coiled-coil region 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-B1AK53-F168.760.38

Human Protein Atlas

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

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): vesicles

Antibody reliability (HPA): IH enhanced · IF approved

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 (6)

TypePositions
Phosphoserine338, 342, 515, 647, 690, 696

Mutagenesis-validated functional residues (2)

PositionPhenotype
790–795no effect on localization to microvilli. no effect on microvillar elongation.
790–795loss of targeting to microvilli. impaired microvillar elongation.

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

IDPathwayEvidence
R-HSA-9709957Sensory Perception—
R-HSA-9659379Sensory processing of sound—
R-HSA-9662360Sensory processing of sound by inner hair cells of the cochleaelectronic
R-HSA-9662361Sensory processing of sound by outer hair cells of the cochleaelectronic

MSigDB gene sets: 211 (showing top): GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, BENPORATH_ES_WITH_H3K27ME3, MODULE_255, RORA1_01, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, MODULE_317, WHITE_NEUROBLASTOMA_WITH_1P36.3_DELETION, GOBP_ACTIN_FILAMENT_ORGANIZATION, GOBP_SENSORY_PERCEPTION, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOMF_ACTIN_BINDING, GOCC_NEURON_PROJECTION, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_MICROVILLUS_ORGANIZATION, WONG_ENDMETRIUM_CANCER_UP

GO Biological Process (3): sensory perception of sound (GO:0007605), microvillar actin bundle assembly (GO:0030034), actin filament bundle assembly (GO:0051017)

GO Molecular Function (4): SH3 domain binding (GO:0017124), actin filament binding (GO:0051015), actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (10): cytoplasm (GO:0005737), microvillus (GO:0005902), brush border (GO:0005903), filamentous actin (GO:0031941), stereocilium (GO:0032420), stereocilium tip (GO:0032426), cytoskeleton (GO:0005856), organelle (GO:0043226), actin-based cell projection (GO:0098858), cluster of actin-based cell projections (GO:0098862)

Reactome top-level categories

2 top-level categories:

CategoryPathways
Sensory processing of sound2
Sensory Perception1

GO top-level categories

25 GO namespaces:

CategoryTerms
cellular anatomical structure4
actin-based cell projection3
sensory perception of mechanical stimulus1
microvillus assembly1
parallel actin filament bundle assembly1
cellular component assembly1
actin filament bundle organization1
protein domain specific binding1
actin binding1
protein-containing complex binding1
cytoskeletal protein binding1
binding1
intracellular anatomical structure1
actin filament bundle1
microvillus1
apical part of cell1
cluster of actin-based cell projections1
actin filament1
protein-containing complex1
stereocilium bundle1
neuron projection1
stereocilium1
intracellular membraneless organelle1
actin cytoskeleton1
plasma membrane bounded cell projection1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 17 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO termNSEvidence
microvillar actin bundle assemblyBPmutant phenotype
microvillusCCdirect assay
stereociliumCCdirect assay

Protein interactions and networks

STRING

showing 15 of 914 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
ESPNFSCN1Q16658917
ESPNGJB2P29033836
ESPNWHRNQ9P202804
ESPNMYO15AQ9UKN7778
ESPNMYO7AP78427725
ESPNMYO3AQ8NEV4723
ESPNE9PNW1E9PNW1716
ESPNPCDH15Q96QU1694
ESPNPLS1Q14651691
ESPNSTRCQ7RTU9683
ESPNEPS8Q12929673
ESPNEPS8L2Q9H6S3668
ESPNCDH23Q9H251646
ESPNMYO3BQ8WXR4636
ESPNTRIOBPQ9H2D6631

IntAct

Human interaction partners of ESPN in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

5 partners by confidence:

PartnerInteraction typeMIscoreRecords
CTSCassociation0.3502
BAIAP2association0.3501
DNAI1association0.3501
PNKDassociation0.3501
RAB37association0.3501

BioGRID (18 interactions; top human partners by supporting records): BAIAP2 (Affinity Capture-MS; 2 records), BAIAP2L1 (Affinity Capture-MS), C17orf70 (Affinity Capture-MS), CTSC (Affinity Capture-MS), DBN1 (Cross-Linking-MS (XL-MS)), DDX24 (Affinity Capture-MS), DDX58 (Affinity Capture-RNA), DNAI1 (Affinity Capture-MS), FAM98A (Affinity Capture-MS), HNRNPL (Affinity Capture-RNA), METTL21B (Affinity Capture-MS), PNKD (Affinity Capture-MS), PRMT2 (Affinity Capture-MS), RAB37 (Affinity Capture-MS), SNRNP40 (Proximity Label-MS)

Disease & clinical

Genetic variants

Variant evidence for ESPN: 699 ClinVar records (36 pathogenic / likely pathogenic); 3 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic14
Likely pathogenic22
Uncertain significance336
Likely benign221
Benign39

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 36 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
450999NM_031475.3(ESPN):c.1464+1G>ALikely pathogeniccriteria provided, multiple submitters, no conflicts2
560535NM_031475.3(ESPN):c.2369_2386del (p.Arg790_Arg795del)Pathogeniccriteria provided, single submitter2
594412NM_031475.3(ESPN):c.264G>A (p.Trp88Ter)Pathogeniccriteria provided, single submitter1
984702NM_031475.3(ESPN):c.1916-1G>CPathogeniccriteria provided, single submitter1
1299307NM_031475.3(ESPN):c.2081_2082del (p.Ser694fs)Pathogeniccriteria provided, single submitter1
2445633NM_031475.3(ESPN):c.2496C>G (p.Tyr832Ter)Pathogeniccriteria provided, single submitter1
2572469NM_031475.3(ESPN):c.1649_1665del (p.Arg550fs)Pathogeniccriteria provided, single submitter1
3601083NM_031475.3(ESPN):c.1916-1G>APathogeniccriteria provided, single submitter1
3601084NM_031475.3(ESPN):c.1995_2056del (p.Lys666fs)Pathogeniccriteria provided, single submitter1
4291998NM_031475.3(ESPN):c.489-2A>GPathogeniccriteria provided, single submitter1
4934024NM_031475.3(ESPN):c.2254_2275del (p.Glu752fs)Pathogeniccriteria provided, single submitter1
4420NM_031475.3(ESPN):c.2155A>C (p.Ser719Arg)Likely pathogeniccriteria provided, single submitter2
4423NM_031475.3(ESPN):c.2539AAG[1] (p.Lys848del)Likely pathogeniccriteria provided, single submitter2
452503NM_031475.3(ESPN):c.292C>T (p.Gln98Ter)Likely pathogeniccriteria provided, single submitter1
623132NM_031475.3(ESPN):c.2446G>T (p.Glu816Ter)Likely pathogeniccriteria provided, single submitter1

Per-variant reference — Sugi Variant

Explore ESPN’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; 35 predictions of 1,571):

Position(s)EffectΔscoreSites
1:6425250–6425251donor_loss1.00004
1:6428416donor_gain1.0000
1:6440252–6440253acceptor_loss1.00004
1:6440614acceptor_gain1.0000
1:6440809–6440810donor_loss1.00005
1:6440932–6440933acceptor_loss1.00003
1:6441066–6441067donor_loss1.00005
1:6448639–6448640acceptor_loss1.00005
1:6448803–6448804donor_loss1.00003
1:6451601–6451602acceptor_loss1.00004

AlphaMissense

1,501 missense substitutions predicted likely pathogenic (of 5,490 scored), across 408 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M64590.8620.982
M20790.8480.967
D27880.9730.988
D10180.9640.990
D7680.9630.976
D30280.9580.983
D26980.9530.982
H24580.9340.973
F64380.9340.995
D23780.9300.983
D74480.9260.982
H27780.9220.978
D3380.9110.940
H7580.9050.957
N28280.9040.983
H4180.8990.963
H10980.8900.975
H14380.8730.953
H21180.8380.951
S24980.8270.992

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Kidney Renal Clear Cell Carcinoma (TCGA)favorable2.97e-05
Kidney Renal Clear Cell Carcinoma (validation)favorable6.16e-05

Disease associations

OMIM: gene MIM:606351 | disease phenotypes: MIM:609006, MIM:621556, MIM:618632, MIM:220290, MIM:607197

GenCC curated gene-disease

5 curated gene-disease records:

DiseaseClassificationInheritanceRecords
autosomal recessive nonsyndromic hearing loss 36DefinitiveAutosomal recessive4
nonsyndromic genetic hearing lossDefinitiveAutosomal recessive4
Usher syndrome type 1SupportiveAutosomal recessive
hearing loss, autosomal recessiveSupportiveAutosomal recessive
Usher syndrome, type 1MLimitedUnknown2

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

2 validity classifications:

DiseaseClassificationInheritance
nonsyndromic genetic hearing lossDefinitiveAR
nonsyndromic genetic hearing lossLimitedAD

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (3 panels, 2 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

3 panels:

PanelRating
Monogenic hearing lossgreen
Paediatric disordersgreen
Retinal disordersamber

Mondo (7): autosomal recessive nonsyndromic hearing loss 36 (MONDO:0012170), inherited retinal dystrophy (MONDO:0019118), autosomal dominant nonsyndromic hearing loss 91 (MONDO:0981166), Usher syndrome, type 1M (MONDO:0032841), Usher syndrome type 1 (MONDO:0010168), hearing loss, autosomal recessive (MONDO:0019588), nonsyndromic genetic hearing loss (MONDO:0019497)

Orphanet (6): Rare autosomal recessive non-syndromic sensorineural deafness type DFNB (Orphanet:90636), Rare genetic deafness (Orphanet:96210), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Usher syndrome type 1 (Orphanet:231169), Usher syndrome (Orphanet:886), Rare autosomal dominant non-syndromic sensorineural deafness type DFNA (Orphanet:90635)

HPO phenotypes

26 phenotypes (HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000375Abnormal cochlea morphology
HP:0000399Prelingual sensorineural hearing impairment
HP:0000407Sensorineural hearing impairment
HP:0000510Rod-cone dystrophy
HP:0000512Abnormal electroretinogram
HP:0000518Cataract
HP:0000543Optic disc pallor
HP:0000572Visual loss
HP:0000575Scotoma
HP:0000662Nyctalopia
HP:0000716Depression
HP:0000739Anxiety
HP:0000750Delayed speech and language development
HP:0001270Motor delay
HP:0001712Left ventricular hypertrophy
HP:0001751Abnormal vestibular function
HP:0002141Gait imbalance
HP:0003596Middle age onset
HP:0007663Reduced visual acuity
HP:0007994Peripheral visual field loss
HP:0008568Vestibular areflexia
HP:0011462Young adult onset
HP:0011463Childhood onset
HP:0011510Drusen

GWAS associations

3 associations:

StudyTraitp-value
GCST009597_120Multiple sclerosis9e-17
GCST005116_11Male-pattern baldness8e-10
GCST010151_8Carotid intima media thickness x smoking interaction6e-6

EFO canonical traits (from GWAS)

1 canonical traits:

EFO IDTrait name
EFO:0006527smoking status measurement

MeSH disease descriptors

4 disease descriptors:

DescriptorNameTree numbers
D058499Retinal DystrophiesC11.768.585.658
C564609Deafness, Autosomal Recessive *(supp.)*
C563815Deafness, Autosomal Recessive 36 *(supp.)*
C580334Nonsyndromic Deafness *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Cyclosporinedecreases methylation, decreases expression4
Genisteinaffects cotreatment, decreases expression, increases expression4
bisphenol Aaffects expression, increases expression3
Air Pollutantsdecreases expression, increases abundance, increases expression3
Benzo(a)pyrenedecreases expression, increases methylation3
Estradiolaffects cotreatment, decreases expression, increases expression3
sodium arseniteincreases expression, decreases expression2
Resveratrolaffects cotreatment, decreases expression, increases expression2
Tobacco Smoke Pollutiondecreases expression2
aristolochic acid Iincreases expression1
daidzeindecreases expression, affects cotreatment1
methyleugenoldecreases expression1
beta-lapachonedecreases expression1
sulforaphanedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
butyraldehydeincreases expression1
benzo(e)pyrenedecreases methylation1
glyciteinaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
licochalcone Bincreases expression1
Rosiglitazonedecreases expression1
Acetaminophendecreases expression1
Caffeineincreases phosphorylation1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Diethylnitrosaminedecreases expression1
Diethylstilbestrolincreases expression1
Endosulfanincreases expression1
Folic Aciddecreases expression1
Leadaffects expression1

Clinical trials (associated diseases)

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

showing 60 of 146 trials:

NCTPhaseStatusTitle
NCT04224207Phase 3COMPLETEDManagement of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855Phase 3NOT_YET_RECRUITINGA Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT01655212Phase 3TERMINATEDCongenital Cytomegalovirus: Efficacy of Antiviral Treatment in a Randomized Controlled Trial
NCT02005822Phase 3COMPLETEDCongenital Cytomegalovirus: Efficacy of Antiviral Treatment
NCT03374514Phase 3UNKNOWNCochlear Electrical Impedance and the Effect of Topical Dexamethasone on Cochlear Implant Surgery
NCT03763227Phase 2COMPLETEDIntravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207Phase 2COMPLETEDMinocycline Treatment in Retinitis Pigmentosa
NCT04945772Phase 2COMPLETEDEfficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT02497690Phase 2COMPLETEDEffectiveness of Therapy Via Telemedicine Following Cochlear Implants
NCT03107871Phase 2TERMINATEDRandomized Controlled Trial of Valganciclovir for Cytomegalovirus Infected Hearing Impaired Infants
NCT04120116Phase 2COMPLETEDFX-322 in Adults With Stable Sensorineural Hearing Loss
NCT05061758Phase 2WITHDRAWNA Trial of LY3056480 in Patients With SNLH
NCT07364747Phase 2RECRUITINGProtective Effect of Acetylcysteine Against Cisplatinum-Induced Ototoxicity: A Randomized Controlled Trial
NCT05902962Phase 1COMPLETEDSAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872Phase 1RECRUITINGThe Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826Phase 1COMPLETEDMAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)
NCT01064505Phase 1COMPLETEDSafety Study of a Single IVT Injection of QPI-1007 in Chronic Optic Nerve Atrophy and Recent Onset NAION Patients
NCT05147701Phase 1RECRUITINGSafety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for NAION
NCT02038972Phase 1COMPLETEDSafety of Autologous Stem Cell Infusion for Children With Acquired Hearing Loss
NCT02259595Phase 1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT01802190Not specifiedTERMINATEDPrevalence of POU4F3 and SLC17A8 Mutations
NCT04855045Phase 2/3UNKNOWNAn Open-label, Dose Escalation and Double-masked, Randomized, Controlled Trial Evaluating Safety and Tolerability of Sepofarsen in Children (<8 Years of Age) With LCA10 Caused by Mutations in the CEP290 Gene.
NCT03872479Phase 1/2UNKNOWNSingle Ascending Dose Study in Participants With LCA10
NCT04123626Phase 1/2ACTIVE_NOT_RECRUITINGA Study to Evaluate the Safety and Tolerability of QR-1123 in Subjects With Autosomal Dominant Retinitis Pigmentosa Due to the P23H Mutation in the RHO Gene
NCT04545736Phase 1/2ACTIVE_NOT_RECRUITINGOral Metformin for Treatment of ABCA4 Retinopathy
NCT06212297Phase 1/2ACTIVE_NOT_RECRUITINGFellow-eye Study (FE) of LX101 in Subjects With Inherited Retinal Dystrophy
NCT06852963Phase 1/2ACTIVE_NOT_RECRUITINGA Repeat-Dose, Open-Label, Two Arm Safety and Efficacy Study of Two Doses of VP-001 Administered Intravitreally in Participants With Confirmed PRPF31 Mutation-Associated Retinal Dystrophy, Including Participants Previously Treated With VP001
NCT07177196Phase 1/2ACTIVE_NOT_RECRUITINGPersonalized Antisense Oligonucleotide Therapy for a Single Participant With PRPH2 Mutation Associated With Retinal Dystrophy
NCT07063030Early Phase 1RECRUITINGA Study of LX107 Gene Therapy in AIPL1-IRD Patients
NCT07656753Early Phase 1RECRUITINGSafety and Efficacy Study of PUMCH-E111 Injection in Subjects With RLBP1 Related Inherited Retinal Dystrophy
NCT01546181Not specifiedCOMPLETEDRetinal Imaging by Adaptive Optics in Healthy Eyes and During Retinal and General Diseases
NCT01876147Not specifiedCOMPLETEDVisual and Functional Assessment in Low Vision Patients
NCT01920867Not specifiedUNKNOWNStem Cell Ophthalmology Treatment Study
NCT02014389Not specifiedRECRUITINGEvaluation of Objective Perimetry Using Chromatic Multifocal Pupillometer
NCT02983305Not specifiedCOMPLETEDOptical Head-Mounted Display Technology for Low Vision Rehabilitation
NCT03592017Not specifiedCOMPLETEDPerformance of Long-wavelength Autofluorescence Imaging
NCT03662386Not specifiedTERMINATEDProspective Analysis of Genotype-phenotype Correlations Observed in a Large Cohort of Patients With Hereditary Retinal Dystrophies - GEPHIRD
NCT03691168Not specifiedUNKNOWNMulti-center Observation of the Natural Course of Inherited Retinal Dystrophies
NCT03843840Not specifiedCOMPLETEDDual Wavelength OCT
NCT03853252Not specifiedCOMPLETEDiPS Cells of Patients for Models of Retinal Dystrophies
NCT05130385Not specifiedUNKNOWNHigh Resolution Optical Coherence Tomography
NCT05294978Not specifiedRECRUITINGEyeConic: Qualification for Cone-Optogenetics
NCT05573984Not specifiedACTIVE_NOT_RECRUITINGNatural History of PRPF31 Mutation-Associated Retinal Dystrophy
NCT05793515Not specifiedCOMPLETEDMechanisms of Inherited Retinal Dystrophies Using Whole Genome Sequencing and in Vitro and in Vivo Models
NCT05820100Not specifiedCOMPLETEDObservational Study to Assess the Reliability and Validity of the MLYMT and MLSDT
NCT05976139Not specifiedRECRUITINGMicropulsed Laser in Patients With Macular Oedema in Retinal Dystrophies
NCT06162585Not specifiedACTIVE_NOT_RECRUITINGNon-Interventional Long Term Follow-up Study of Participants Previously Enrolled in the RESTORE Study
NCT06177977Not specifiedRECRUITINGSS-HH-OCT as a Novel Diagnostic Modality for Early-Onset Retinal Dystrophies (EORDs)
NCT06375239Not specifiedRECRUITINGObservational Study to Assess Endpoint Operational Feasibility & Measurement Properties in Patients with Retinal Degeneration
NCT06908161Not specifiedNOT_YET_RECRUITINGFunctional Assessments in Vision Impairment
NCT07085533Not specifiedRECRUITINGNatural History Study of Inherited Retinal Diseases
NCT07502664Not specifiedRECRUITINGDevelopment and Evaluation of Functional Visual Field and Navigation Endpoints in Moderate to Profound Inherited Retinal Disease (DEFINE-IRD)
NCT07529041Not specifiedENROLLING_BY_INVITATIONReal-time Acoustic Biofeedback for Enhancing Fixation Stability: A Proof-of-concept Study to Improve Ophthalmic Imaging Diagnostic Quality
NCT02882477Phase 2/3UNKNOWNTreatment of Wolfram Syndrome Type 2 With the Chelator Deferiprone and Incretin Based Therapy
NCT01834079Phase 1/2UNKNOWNStudy the Safety and Efficacy of Bone Marrow Derived Autologous Cells for the Treatment of Optic Nerve Disease
NCT04680143Phase 1/2COMPLETEDSystemic Erythropoietin Injection in Patients Having Optic Atrophy
NCT03011541Not specifiedRECRUITINGStem Cell Ophthalmology Treatment Study II
NCT04580979Not specifiedCOMPLETEDNatural History Study of FDXR Mutation-related Mitochondriopathy
NCT04594590Not specifiedCOMPLETEDNatural History Study of SLC25A46 Mutation-related Mitochondriopathy
NCT04723160Not specifiedCOMPLETEDComputer Aided Diagnosis of Multiple Eye Fundus Diseases From Color Fundus Photograph