MORN3

protein-coding

MORN repeat containing 3

Gene summary

Enables protein-macromolecule adaptor activity. Involved in negative regulation of signal transduction by p53 class mediator. Located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_173855.5

Inheritance

—

ClinVar variants

P:1U:50B:4

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr12:121,648,742-121,672,631

External References & Databases

Ensembl (ENSG00000139714)

Transcript & Mutation Effects

hg38 • Region Span ~23.9 kb

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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 MORN3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 2

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173855.5. 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			1 clinvar			1
missense			48 clinvar	3 clinvar	1 clinvar	52
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	50	3	1	55

Highest pathogenic variant AF is 0.000021687834

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173855.5	RefSeq	NP_776254.3	5	MANE Select
ENST00000355329.7	Ensembl	ENSP00000347486.3	5	MANE Select
NM_001363685.2	RefSeq	NP_001350614.1	5	Standard
ENST00000392462.6	Ensembl	ENSP00000376255.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355329
Coding exons: 5
Length: 21514
Individuals with no LoFs: 125665
Homozygous LoFs: 0
Heterozygous LoFs: 82
Defined: 125747
p: 0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.616	129	150	0.859	0.00000944	1571
Missense (PolyPhen)		46	48.734	0.94391		432
Synonymous	0.413	55	59.0	0.932	0.00000428	404
Loss of Function	0.705	12	14.9	0.803	7.23e-7	163

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.0022	0.0022	notable
East Asian	0.00093	0.00087	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00028	0.00026	rare
South Asian	0.00011	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.725
RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.214

Gene Damage Prediction

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