MON1A

MON1 homolog A, secretory trafficking associated

Basic information

Region (hg38): 3:49907160-49930173

Links

ENSG00000164077 ∙ NCBI:84315 ∙ OMIM:611464 ∙ HGNC:28207 ∙ Uniprot:Q86VX9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MON1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MON1A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	43			44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	1		9
Total	0	1	51	1	0

Variants in MON1A

This is a list of pathogenic ClinVar variants found in the MON1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-49909030-G-A		not specified	Uncertain significance (Mar 26, 2024)
3-49909042-A-T		not specified	Uncertain significance (May 09, 2023)
3-49909045-C-T		not specified	Uncertain significance (Nov 20, 2023)
3-49909069-C-T		not specified	Uncertain significance (Aug 16, 2021)
3-49909094-C-T		not specified	Uncertain significance (Dec 03, 2021)
3-49909144-G-A		not specified	Uncertain significance (Oct 06, 2022)
3-49909272-T-C		not specified	Uncertain significance (Dec 11, 2023)
3-49909306-G-T		not specified	Uncertain significance (Aug 20, 2024)
3-49909323-C-T		not specified	Uncertain significance (Aug 05, 2024)
3-49909392-A-G		not specified	Uncertain significance (Feb 05, 2024)
3-49910203-G-A		not specified	Uncertain significance (Feb 14, 2024)
3-49910206-C-T		not specified	Uncertain significance (Nov 17, 2022)
3-49910207-G-A		not specified	Uncertain significance (Jan 10, 2023)
3-49910212-G-A		not specified	Uncertain significance (Feb 10, 2025)
3-49910216-C-G		not specified	Uncertain significance (Dec 05, 2024)
3-49910332-G-C		not specified	Uncertain significance (Mar 29, 2022)
3-49910351-A-C		not specified	Uncertain significance (Oct 06, 2023)
3-49910386-T-C		not specified	Uncertain significance (May 26, 2022)
3-49910410-G-A		not specified	Uncertain significance (May 16, 2023)
3-49910521-C-T		not specified	Uncertain significance (Aug 01, 2022)
3-49910557-C-T		not specified	Uncertain significance (Aug 12, 2024)
3-49910762-G-A		not specified	Uncertain significance (Jan 24, 2025)
3-49910864-C-G		not specified	Uncertain significance (Mar 08, 2025)
3-49911556-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-49911586-T-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MON1A	protein_coding	protein_coding	ENST00000296473	6	21305

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.30e-9	0.688	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	323	434	0.745	0.0000286	4168
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000501	0.000499
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000960	0.0000924
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.000233	0.000229
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.118
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

• pHI: 0.283
• hipred: N
• hipred_score: 0.486
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.423

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mon1a

Gene ontology

• Biological process: protein secretion
• Cellular component: cytosol;Mon1-Ccz1 complex
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding