MGRN1

mahogunin ring finger 1, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 16:4616492-4690974

Links

ENSG00000102858 ∙ NCBI:23295 ∙ OMIM:607559 ∙ HGNC:20254 ∙ Uniprot:O60291 ∙ 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 MGRN1 gene.

• Inborn genetic diseases (35 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGRN1 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				4	1	5
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	34	7	1

Variants in MGRN1

This is a list of pathogenic ClinVar variants found in the MGRN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4624967-T-A		not specified	Uncertain significance (Aug 17, 2022)
16-4650413-C-T		not specified	Uncertain significance (Aug 09, 2021)
16-4650417-C-A			Benign (Dec 31, 2019)
16-4650448-A-G		not specified	Uncertain significance (Jan 23, 2023)
16-4650466-G-A		not specified	Uncertain significance (Aug 22, 2023)
16-4651987-C-A		not specified	Uncertain significance (May 05, 2023)
16-4652003-C-T		not specified	Uncertain significance (May 03, 2023)
16-4652027-G-A		not specified	Uncertain significance (May 26, 2023)
16-4652694-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-4652757-G-A		not specified	Uncertain significance (Jan 27, 2022)
16-4652760-G-A		not specified	Uncertain significance (Aug 08, 2023)
16-4652766-C-T		not specified	Uncertain significance (Jun 09, 2022)
16-4652767-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-4652820-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-4657257-A-G		not specified	Uncertain significance (Jun 09, 2022)
16-4657281-C-G		not specified	Uncertain significance (Dec 21, 2021)
16-4657283-G-A		not specified	Uncertain significance (Feb 06, 2024)
16-4657290-A-G		not specified	Uncertain significance (Oct 26, 2022)
16-4664727-C-G		not specified	Uncertain significance (Feb 17, 2022)
16-4664733-G-A		not specified	Uncertain significance (Mar 11, 2024)
16-4664772-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-4665130-G-C			Likely benign (Jun 01, 2022)
16-4668274-G-A		not specified	Uncertain significance (Aug 13, 2021)
16-4673498-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-4673551-C-T			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGRN1	protein_coding	protein_coding	ENST00000262370	17	74482

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.104	0.896	125613	0	21	125634	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.55	457	373	1.23	0.0000247	3710
Missense in Polyphen		152	141.79	1.072		1456
Synonymous	-4.63	254	176	1.44	0.0000139	1152
Loss of Function	3.83	8	31.1	0.258	0.00000160	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000892	0.0000880
Middle Eastern	0.000110	0.000109
South Asian	0.000131	0.000131
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase. Mediates monoubiquitination at multiple sites of TSG101 in the presence of UBE2D1, but not of UBE2G1, nor UBE2H. Plays a role in the regulation of endosome-to- lysosome trafficking. Impairs MC1R- and MC4R-signaling by competing with GNAS-binding to MCRs and inhibiting agonist-induced cAMP production. Does not inhibit ADRB2-signaling. Does not promote MC1R ubiquitination. Acts also as a negative regulator of hedgehog signaling (By similarity). {ECO:0000250|UniProtKB:Q9D074, ECO:0000269|PubMed:17229889, ECO:0000269|PubMed:19703557, ECO:0000269|PubMed:19737927}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.500
• rvis_EVS: -1.77
• rvis_percentile_EVS: 2.3

Haploinsufficiency Scores

• pHI: 0.491
• hipred: Y
• hipred_score: 0.756
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgrn1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype; embryo phenotype; respiratory system phenotype; homeostasis/metabolism phenotype; muscle phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: protein polyubiquitination;protein monoubiquitination;endosome to lysosome transport;negative regulation of cAMP-mediated signaling;negative regulation of G protein-coupled receptor signaling pathway;negative regulation of smoothened signaling pathway
• Cellular component: nucleus;cytoplasm;early endosome;cytosol;plasma membrane;membrane;extracellular exosome
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding;ubiquitin protein ligase activity