MGRN1

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

Basic information

Region (hg38): 16:4616493-4690974

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.

not_specified (121 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. These statistics are base on transcript: NM_000015246.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	4 clinvar	1 clinvar	8
missense			116 clinvar	6 clinvar		122
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	130	10	1

Loading clinvar variants...

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
		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

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

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