OTOR

Summary

OTOR (otoraplin, HGNC:8517) is a protein-coding gene on chromosome 20p12.1, encoding Otoraplin (Q9NRC9).

This gene encodes a member of the melanoma-inhibiting activity gene family. The encoded protein is secreted via the Golgi apparatus and may function in cartilage development and maintenance. A frequent polymorphism in the translation start codon of this gene can abolish translation and may be associated with forms of deafness.

Source: NCBI Gene 56914 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_020157

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8517
Approved symbol	OTOR
Name	otoraplin
Location	20p12.1
Locus type	gene with protein product
Status	Approved
Aliases	MIAL, MIAL1, FDP
Ensembl gene	ENSG00000125879
Ensembl biotype	protein_coding
OMIM	606067
Entrez	56914

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000246081, ENST00000486129, ENST00000490148

RefSeq mRNA: 1 — MANE Select: NM_020157 NM_020157

CCDS: CCDS13124

Canonical transcript exons

ENST00000246081 — 4 exons

Exon	Start	End
ENSE00000859189	16748358	16748516
ENSE00000859190	16748867	16749006
ENSE00000859191	16749903	16750010
ENSE00001028103	16751095	16752164

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 80.87.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cochlea	UBERON:0001844	80.87	gold quality
cervix squamous epithelium	UBERON:0006922	72.36	gold quality
type B pancreatic cell	CL:0000169	71.80	gold quality
diaphragm	UBERON:0001103	70.76	gold quality
olfactory bulb	UBERON:0002264	70.13	gold quality
tongue squamous epithelium	UBERON:0006919	70.02	silver quality
epithelial cell of pancreas	CL:0000083	69.51	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	68.18	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	67.17	gold quality
hair follicle	UBERON:0002073	65.12	gold quality
vastus lateralis	UBERON:0001379	64.89	gold quality
vena cava	UBERON:0004087	64.73	silver quality
gluteal muscle	UBERON:0002000	64.59	gold quality
quadriceps femoris	UBERON:0001377	64.13	gold quality
triceps brachii	UBERON:0001509	63.57	gold quality
endothelial cell	CL:0000115	63.02	gold quality
parotid gland	UBERON:0001831	62.94	gold quality
biceps brachii	UBERON:0001507	61.16	gold quality
pericardium	UBERON:0002407	61.00	gold quality
cerebellar vermis	UBERON:0004720	60.96	gold quality
heart right ventricle	UBERON:0002080	60.45	gold quality
myocardium	UBERON:0002349	60.16	gold quality
deltoid	UBERON:0001476	59.68	gold quality
buccal mucosa cell	CL:0002336	59.37	gold quality
cartilage tissue	UBERON:0002418	59.03	gold quality
Brodmann (1909) area 46	UBERON:0006483	59.01	gold quality
body of tongue	UBERON:0011876	58.94	gold quality
decidua	UBERON:0002450	58.65	gold quality
gingiva	UBERON:0001828	58.35	gold quality
squamous epithelium	UBERON:0006914	58.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting OTOR, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-1275	99.47	67.90	2749

Literature-anchored findings (GeneRIF, showing 1)

• results indicate that OTOR plays a crucial role in the progression of and prognosis for breast carcinoma (BC), which could help to identify future therapeutic targets for treating BC patients (PMID:30897334)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Otor	ENSMUSG00000027416
rattus_norvegicus	Otor	ENSRNOG00000028721
drosophila_melanogaster	Tango1	FBGN0286898

Paralogs (10): MIA2 (ENSG00000150527), MIA3 (ENSG00000154305), SPZ1 (ENSG00000164299), CTAGE1 (ENSG00000212710), CTAGE9 (ENSG00000236761), MIA (ENSG00000261857), CTAGE15 (ENSG00000271079), CTAGE6 (ENSG00000271321), CTAGE4 (ENSG00000288784), CTAGE8 (ENSG00000289604)

Protein

Protein identifiers

Otoraplin — Q9NRC9 (reviewed: Q9NRC9)

Alternative names: Fibrocyte-derived protein, Melanoma inhibitory activity-like protein

All UniProt accessions (1): Q9NRC9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Tissue specificity. Highly expressed in cochlea.

Similarity. Belongs to the MIA/OTOR family.

RefSeq proteins (1): NP_064542* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001452	SH3_domain	Domain
IPR035554	Otoraplin_SH3	Domain
IPR036028	SH3-like_dom_sf	Homologous_superfamily
IPR042801	OTOR	Family

Pfam: PF07653

UniProt features (6 total): disulfide bond 2, signal peptide 1, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NRC9-F1	89.09	0.74

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (2): 32–37, 55–127

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 53 (showing top): GOBP_CARTILAGE_DEVELOPMENT, CCAWYNNGAAR_UNKNOWN, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, MODULE_255, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, MODULE_317, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_CELL_AGGREGATION, GOBP_SENSORY_PERCEPTION, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_MORPHOGENESIS, MODULE_69, MODULE_49, MODULE_37, ABE_INNER_EAR

GO Biological Process (2): cartilage condensation (GO:0001502), sensory perception of sound (GO:0007605)

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

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
skeletal system morphogenesis	1
cartilage development	1
cell aggregation	1
sensory perception of mechanical stimulus	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

366 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OTOR	OTOS	Q8NHW6	541
OTOR	CTAGE9	A4FU28	509
OTOR	ATP5PF	P18859	506
OTOR	CTAGE15	A4D2H0	476
OTOR	CTAGE6	Q86UF2	447
OTOR	CHRNA10	Q9GZZ6	447
OTOR	SPAG4	Q9NPE6	439
OTOR	CTAGE8	P0CG41	433
OTOR	OTOA	Q7RTW8	431
OTOR	BAG6	P46379	418
OTOR	CLDN17	P56750	418
OTOR	SNX3	O60493	404
OTOR	UBE4A	Q14139	400
OTOR	OC90	Q02509	397
OTOR	SLC46A2	Q9BY10	391

IntAct

5 interactions, top by confidence:

A	B	Type	Score
FAM209A	OTOR	psi-mi:“MI:0915”(physical association)	0.560
ADAM10	OTOR	psi-mi:“MI:0407”(direct interaction)	0.440
OTOR	FAM209A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (1): OTOR (Two-hybrid)

ESM2 similar proteins: A0A8M9PFP2, A6NFU0, A7UA95, B0S5G3, B5KFD7, D4ACE5, E7F221, E7FCN8, O14525, P59240, P82350, Q0VCN6, Q13145, Q14B46, Q16586, Q16674, Q28038, Q28686, Q5R9Q9, Q5RJL6, Q61137, Q61865, Q62946, Q64255, Q6V7V2, Q7ZV46, Q8C6B2, Q8HYZ0, Q8R553, Q8VDA1, Q8VE43, Q91XN4, Q92918, Q99JH7, Q99KF0, Q99MQ3, Q9BQT9, Q9BST9, Q9BXL6, Q9BXM7

Diamond homologs: Q0VC16, Q16674, Q28038, Q5JRA6, Q61865, Q62946, Q8BI84, Q9I8P5, Q9I8P6, Q9JIE3, Q9NRC9, P52735, Q60992, Q96PC5, Q9R0C8, Q9UKW4, A4D2H0, A4FU28, P0CG41, Q86UF2, Q8IX94, Q8IX95, Q91ZV0, Q96RT6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

433 predictions. Top by Δscore:

Variant	Effect	Δscore
20:16748505:A:G	donor_gain	1.0000
20:16748509:GTGT:G	donor_gain	1.0000
20:16748513:GTCT:G	donor_gain	1.0000
20:16748517:G:GG	donor_gain	1.0000
20:16749005:GT:G	donor_gain	1.0000
20:16749002:GCAGT:G	donor_gain	0.9900
20:16748516:TG:T	donor_loss	0.9800
20:16748517:GT:G	donor_loss	0.9800
20:16748522:G:GT	donor_gain	0.9800
20:16748861:TTCCA:T	acceptor_loss	0.9800
20:16748863:CCA:C	acceptor_loss	0.9800
20:16748865:A:AG	acceptor_gain	0.9800
20:16748865:A:T	acceptor_loss	0.9800
20:16748866:G:GG	acceptor_gain	0.9800
20:16748866:GATA:G	acceptor_gain	0.9800
20:16751094:GGAT:G	acceptor_gain	0.9800
20:16748508:A:AG	donor_gain	0.9700
20:16748514:TCT:T	donor_gain	0.9700
20:16748866:GAT:G	acceptor_gain	0.9700
20:16749007:G:GG	donor_gain	0.9700
20:16749012:A:G	donor_gain	0.9700
20:16749892:T:TA	acceptor_gain	0.9700
20:16750580:A:G	donor_gain	0.9700
20:16751089:TTCCA:T	acceptor_loss	0.9700
20:16751090:TCCA:T	acceptor_loss	0.9700
20:16751091:CCAGG:C	acceptor_loss	0.9700
20:16751092:CAGGA:C	acceptor_loss	0.9700
20:16751093:A:AT	acceptor_loss	0.9700
20:16751094:G:GT	acceptor_loss	0.9700
20:16749996:G:GT	donor_gain	0.9600

AlphaMissense

840 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:16748920:T:C	F57L	0.995
20:16748922:C:A	F57L	0.995
20:16748922:C:G	F57L	0.995
20:16749946:T:G	F100C	0.995
20:16751104:T:C	F125L	0.995
20:16751106:C:A	F125L	0.995
20:16751106:C:G	F125L	0.995
20:16748495:T:A	C32S	0.992
20:16748496:G:C	C32S	0.992
20:16748997:G:C	W82C	0.992
20:16748997:G:T	W82C	0.992
20:16749946:T:C	F100S	0.992
20:16748510:T:A	C37S	0.990
20:16748511:G:C	C37S	0.990
20:16748921:T:G	F57C	0.990
20:16748959:T:C	S70P	0.989
20:16748995:T:A	W82R	0.989
20:16748995:T:C	W82R	0.989
20:16751105:T:G	F125C	0.989
20:16748510:T:C	C37R	0.988
20:16748875:T:C	S42P	0.987
20:16749945:T:C	F100L	0.987
20:16749947:C:A	F100L	0.987
20:16749947:C:G	F100L	0.987
20:16748921:T:C	F57S	0.986
20:16748497:T:G	C32W	0.985
20:16751110:T:A	C127S	0.985
20:16751111:G:A	C127Y	0.985
20:16751111:G:C	C127S	0.985
20:16748496:G:A	C32Y	0.983

dbSNP variants (sampled 300 via entrez): RS1000507563 (20:16751990 T>A), RS1001035878 (20:16747746 A>C,G,T), RS1001165553 (20:16748116 C>T), RS1001371333 (20:16747026 T>C), RS1002150825 (20:16747331 A>G), RS1002782730 (20:16750059 G>A), RS1003824911 (20:16748739 T>C,G), RS1004916294 (20:16749204 G>T), RS1005739771 (20:16749746 T>A), RS1006731092 (20:16751913 A>C), RS1006928585 (20:16746613 G>A,T), RS1007042611 (20:16750348 A>C), RS1007110871 (20:16752304 G>A,T), RS1007703084 (20:16750976 T>A,G), RS1008628509 (20:16747727 G>A)

Disease associations

OMIM: gene MIM:606067 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST002037_4	Post-traumatic stress disorder (asjusted for relatedness)	4.000000e-06
GCST003488_10	Response to fenofibrate (triglyceride levels)	4.000000e-06
GCST003771_7	Loneliness	3.000000e-06
GCST007576_439	Chronotype	2.000000e-07
GCST008338_3	Blood cell traits (multivariate analysis)	7.000000e-10

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0007681	triglyceride change measurement
EFO:0007865	loneliness measurement
EFO:0008328	chronotype measurement
EFO:0004305	erythrocyte count
EFO:0004309	platelet count
EFO:0004528	mean corpuscular hemoglobin concentration
EFO:0004833	neutrophil count
EFO:0004842	eosinophil count
EFO:0005090	basophil count
EFO:0005091	monocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tetrachlorodibenzodioxin	increases expression	2
2-palmitoylglycerol	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Tretinoin	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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