GeneBe

MGRN1

protein-coding

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

Gene summary

Enables protein sequestering activity and ubiquitin-protein transferase activity. Involved in endosome to lysosome transport; negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway; and protein monoubiquitination. Located in early endosome; nucleus; and plasma membrane. Is active in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015246.4

Inheritance

—

ClinVar variants

U:131B:11

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr16:4,616,493-4,690,974

External References & Databases

Ensembl (ENSG00000102858)NCBI Gene (23295)OMIM (607559)HGNC:20254GenCCUniProt (O60291)AlphaFoldClinVar (MGRN1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~74.5 kb
Loading mutation effect viewer...

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 MGRN1 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 121
not providedTotal: 8
See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015246.4. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
4
clinvar
1
clinvar
 8
missense
117
clinvar
6
clinvar
 123
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
11
clinvar
 11
Total00131101142
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015246.4RefSeqNP_056061.117MANE Select
ENST00000262370.12EnsemblENSP00000262370.617MANE Select
NM_001142289.3RefSeqNP_001135761.216Standard
NM_001142290.3RefSeqNP_001135762.117Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ubiquitin mediated proteolysis - Homo sapiens (human)
  • Immune System
  • Adaptive Immune System
  • Antigen processing: Ubiquitination & Proteasome degradation
  • Class I MHC mediated antigen processing & presentation

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

Molecular Function

  • ubiquitin-protein transferase activity
  • protein binding
  • metal ion binding
  • ubiquitin protein ligase activity

Cellular Component

  • nucleus
  • cytoplasm
  • early endosome
  • cytosol
  • plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000262370
Coding exons
17
Length
74482
Individuals with no LoFs
125613
Homozygous LoFs
0
Heterozygous LoFs
21
Defined
125634
p
0.0000836
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-1.554573731.230.00002473710
Missense (PolyPhen)152141.791.0721456
Synonymous-4.632541761.440.00001391152
Loss of Function3.83831.10.2580.00000160350

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000890.000088rare
South Asian0.000130.00013rare
Other0.000170.00016rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.143

Intolerance Scores

LoFtool
0.500
RVIS EVS
-1.77
RVIS percentile EVS
2.3

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.947

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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