MON2

protein-coding

MON2 homolog, regulator of endosome-to-Golgi trafficking, the group of Armadillo like helical domain containing

Gene summary

Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in Golgi to endosome transport; protein targeting to vacuole; and retrograde transport, endosome to Golgi. Located in Golgi apparatus and early endosome membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015026.3

Inheritance

—

ClinVar variants

U:171B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr12:62,466,817-62,600,476

External References & Databases

Ensembl (ENSG00000061987)

Transcript & Mutation Effects

hg38 • Region Span ~133.7 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 MON2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 157

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015026.3. 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			5 clinvar	3 clinvar		8
missense			159 clinvar	2 clinvar		161
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	171	5	0	176

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015026.3	RefSeq	NP_055841.2	35	MANE Select
ENST00000393630.8	Ensembl	ENSP00000377250.4	35	MANE Select
NM_001278469.3	RefSeq	NP_001265398.1	35	Standard
NM_001278470.2	RefSeq	NP_001265399.1	34	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

Golgi to endosome transport
protein transport

Molecular Function

protein binding

Cellular Component

cytosol
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393632
Coding exons: 35
Length: 130767
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125748
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.20	607	873	0.695	0.0000418	11138
Missense (PolyPhen)		146	278.22	0.52477		3669
Synonymous	0.330	300	307	0.976	0.0000150	3381
Loss of Function	6.88	20	90.8	0.220	0.00000454	1112

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be required for traffic between late Golgi and early endosomes. {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.652
RVIS EVS: -0.83
RVIS percentile EVS: 11.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: N
Indispensability score: 0.443

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High