GeneBe

MCOLN3

mucolipin TRP cation channel 3, the group of Transient receptor potential cation channels

Basic information

Region (hg38): 1:85018082-85048500

Links

ENSG00000055732 ∙ NCBI:55283 ∙ OMIM:607400 ∙ HGNC:13358 ∙ Uniprot:Q8TDD5 ∙ 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 MCOLN3 gene.

  • not_specified (61 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCOLN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018298.11. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
60
clinvar
1
clinvar
 61
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 60 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MCOLN3protein_codingprotein_codingENST00000370589 1230418
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.32e-110.87012560421421257480.000573
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6232602900.8970.00001423704
Missense in Polyphen7384.5080.863831087
Synonymous1.43821000.8190.00000498981
Loss of Function1.822132.10.6540.00000187352

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009950.000993
Ashkenazi Jewish0.0001090.0000992
East Asian0.0003280.000326
Finnish0.000.00
European (Non-Finnish)0.0002290.000229
Middle Eastern0.0003280.000326
South Asian0.002950.00285
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Nonselective ligand-gated cation channel probably playing a role in the regulation of membrane trafficking events. Acts as Ca(2+)-permeable cation channel with inwardly rectifying activity (PubMed:18369318, PubMed:19497048, PubMed:19522758, PubMed:19885840, PubMed:29106414). Mediates release of Ca(2+) from endosomes to the cytoplasm, contributes to endosomal acidification and is involved in the regulation of membrane trafficking and fusion in the endosomal pathway (PubMed:21245134). Does not seem to act as mechanosensory transduction channel in inner ear sensory hair cells. Proposed to play a critical role at the cochlear stereocilia ankle-link region during hair-bundle growth (By similarity). Involved in the regulation of autophagy (PubMed:19522758). Through association with GABARAPL2 may be involved in autophagosome formation possibly providing Ca(2+) for the fusion process (By similarity). Through a possible and probably tissue-specific heteromerization with MCOLN1 may be at least in part involved in many lysosome-dependent cellular events (PubMed:19885840). Possible heteromeric ion channel assemblies with TRPV5 show pharmacological similarity with TRPML3 (PubMed:23469151). {ECO:0000250|UniProtKB:Q8R4F0, ECO:0000269|PubMed:18369318, ECO:0000269|PubMed:19497048, ECO:0000269|PubMed:19522758, ECO:0000269|PubMed:19885840, ECO:0000269|PubMed:20378547, ECO:0000269|PubMed:21245134, ECO:0000269|PubMed:23469151, ECO:0000269|PubMed:29106414, ECO:0000305}.;
Pathway
Stimuli-sensing channels;Ion channel transport;Transport of small molecules;TRP channels (Consensus)

Recessive Scores

pRec
0.133

Intolerance Scores

loftool
0.582
rvis_EVS
-0.69
rvis_percentile_EVS
15.12

Haploinsufficiency Scores

pHI
0.102
hipred
N
hipred_score
0.476
ghis
0.555

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.210

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mcoln3
Phenotype
growth/size/body region 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); reproductive system phenotype; pigmentation phenotype; limbs/digits/tail 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); hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);

Gene ontology

Biological process
locomotory behavior;inner ear auditory receptor cell differentiation;release of sequestered calcium ion into cytosol;calcium ion transmembrane transport
Cellular component
autophagosome membrane;lysosomal membrane;plasma membrane;integral component of membrane;early endosome membrane;late endosome membrane
Molecular function
calcium channel activity;lipid binding;NAADP-sensitive calcium-release channel activity