MON2

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

Basic information

Region (hg38): 12:62466817-62600476

Links

ENSG00000061987 ∙ NCBI:23041 ∙ OMIM:616822 ∙ HGNC:29177 ∙ Uniprot:Q7Z3U7 ∙ 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 MON2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MON2 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				1		1
missense			78	2		80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	78	3	0

Variants in MON2

This is a list of pathogenic ClinVar variants found in the MON2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-62467220-A-G		not specified	Uncertain significance (Oct 02, 2023)
12-62467261-G-C		not specified	Uncertain significance (Nov 14, 2023)
12-62484182-G-A		not specified	Uncertain significance (Mar 14, 2023)
12-62484213-G-A		not specified	Uncertain significance (Jan 06, 2023)
12-62493981-A-G		not specified	Uncertain significance (Oct 06, 2021)
12-62494025-C-T		not specified	Uncertain significance (Jun 11, 2024)
12-62500828-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-62501592-A-C		not specified	Uncertain significance (Dec 28, 2023)
12-62501682-C-T		not specified	Uncertain significance (Apr 19, 2023)
12-62508297-T-G		not specified	Uncertain significance (Dec 23, 2024)
12-62508398-C-A		not specified	Uncertain significance (Oct 27, 2022)
12-62508421-A-G		not specified	Uncertain significance (Apr 07, 2022)
12-62508429-G-A		not specified	Uncertain significance (Feb 13, 2025)
12-62524585-G-A		not specified	Uncertain significance (Dec 07, 2023)
12-62525134-G-A		not specified	Uncertain significance (Dec 08, 2024)
12-62525184-C-T		not specified	Uncertain significance (Aug 10, 2021)
12-62525185-C-T		not specified	Uncertain significance (Dec 10, 2024)
12-62525996-A-G		not specified	Uncertain significance (Sep 02, 2024)
12-62526020-A-G		not specified	Uncertain significance (Mar 02, 2023)
12-62526083-G-T		not specified	Uncertain significance (Oct 11, 2024)
12-62535577-G-A		not specified	Uncertain significance (Dec 28, 2024)
12-62535626-C-T		not specified	Uncertain significance (Sep 14, 2022)
12-62535671-T-C		not specified	Uncertain significance (Jul 26, 2023)
12-62535695-C-T		not specified	Uncertain significance (Mar 25, 2024)
12-62537159-G-A		not specified	Likely benign (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MON2	protein_coding	protein_coding	ENST00000393632	35	130767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.594	0.406	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.20	607	873	0.695	0.0000418	11138
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000545	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000198	0.000193
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000329	0.0000327
Other	0.000169	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.371
• hipred: Y
• hipred_score: 0.575
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.443

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mon2

Gene ontology

• Biological process: Golgi to endosome transport;protein transport
• Cellular component: cytosol;extracellular exosome
• Molecular function: protein binding