MON1A

protein-coding

MON1 homolog A, secretory trafficking associated

Gene summary

Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in protein secretion. Predicted to act upstream of or within intracellular iron ion homeostasis and protein transport. Part of Mon1-Ccz1 complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032355.4

Inheritance

—

ClinVar variants

P:1U:80

Top phenotype

Congenital diarrhea

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr3:49,907,160-49,930,173

External References & Databases

Ensembl (ENSG00000164077)

Transcript & Mutation Effects

hg38 • Region Span ~23.0 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 MON1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

Congenital diarrheaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032355.4. 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						0
missense		1 clinvar	78 clinvar			79
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	80	0	0	81

Highest pathogenic variant AF is 0.000032838037

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032355.4	RefSeq	NP_115731.3	5	MANE Select
ENST00000296473.8	Ensembl	ENSP00000296473.4	5	MANE Select
NM_001142501.2	RefSeq	NP_001135973.2	4	Standard
ENST00000417270.2	Ensembl	ENSP00000399613.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Rab regulation of trafficking
RAB GEFs exchange GTP for GDP on RABs

Biological Process

protein secretion

Molecular Function

guanyl-nucleotide exchange factor activity
protein binding

Cellular Component

cytosol
Mon1-Ccz1 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296473
Coding exons: 6
Length: 21305
Individuals with no LoFs: 125693
Homozygous LoFs: 0
Heterozygous LoFs: 55
Defined: 125748
p: 0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.89	323	434	0.745	0.0000286	4168
Missense (PolyPhen)		107	169.41	0.63162		1672
Synonymous	1.73	155	185	0.839	0.0000120	1413
Loss of Function	1.38	17	24.3	0.699	0.00000138	242

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00023	0.00023	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays an important role in membrane trafficking through the secretory apparatus. Not involved in endocytic trafficking to lysosomes (By similarity). Acts in concert with CCZ1, as a guanine exchange factor (GEF) for RAB7, promotes the exchange of GDP to GTP, converting it from an inactive GDP-bound form into an active GTP-bound form (PubMed:23084991). {ECO:0000250|UniProtKB:Q6PDG8, ECO:0000269|PubMed:23084991}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.118
RVIS EVS: -0.58
RVIS percentile EVS: 18.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.423

Gene Damage Prediction

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