OTOR

protein-coding

otoraplin, the group of MIA family

Gene summary

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. [provided by RefSeq, Jul 2013]

MANE transcript

NM_020157.4

Inheritance

—

ClinVar variants

U:12B:4

Top phenotype

OTOR-related disorder

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr20:16,748,358-16,770,062

External References & Databases

Ensembl (ENSG00000125879)

Transcript & Mutation Effects

hg38 • Region Span ~21.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OTOR variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 14

not providedTotal: 1

OTOR-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020157.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			12 clinvar	2 clinvar		14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	12	4	0	16

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020157.4	RefSeq	NP_064542.1	4	MANE Select
ENST00000246081.3	Ensembl	ENSP00000246081.3	4	MANE Select
XM_017027959.3	RefSeq	XP_016883448.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cartilage condensation
sensory perception of sound

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000246081
Coding exons: 4
Length: 21705
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125736
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.458	82	71.1	1.15	0.00000385	829
Missense (PolyPhen)		26	23.387	1.1117		287
Synonymous	-0.207	27	25.7	1.05	0.00000157	230
Loss of Function	0.718	4	5.88	0.680	2.45e-7	85

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00037	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000053	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.128

Intolerance Scores

LoFtool: 0.486
RVIS EVS: 0.39
RVIS percentile EVS: 75.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.185

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium