TRPM3
Basic information
Region (hg38): 9:70529059-71446904
Links
Phenotypes
GenCC
Source:
- schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
- autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
- schizophrenia (Limited), mode of inheritance: AD
- intellectual disability (Limited), mode of inheritance: AD
- cataract-glaucoma syndrome (Limited), mode of inheritance: AD
- neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures (Strong), mode of inheritance: AD
- cataract 50 with or without glaucoma (Strong), mode of inheritance: AD
- neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Cataract 50 with or without glaucoma | AD | Ophthalmologic | The condition can include risk of glaucoma, and awareness may allow surveillance and early management | Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 25090642,; 31278393; 32343227; 32439617; 32427099; 33484482; 34438093; 35146895 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (84 variants)
- Inborn genetic diseases (34 variants)
- TRPM3-related condition (4 variants)
- Neurodevelopmental disorder (3 variants)
- Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures (3 variants)
- not specified (2 variants)
- Developmental disorder (1 variants)
- TRPM3-associated epilepsy syndrome (1 variants)
- Birk-Barel syndrome (1 variants)
- See cases (1 variants)
- TRPM3 related neruodevelopmental disorder (1 variants)
- Mulibrey nanism syndrome (1 variants)
- Intellectual disability;Epileptic encephalopathy (1 variants)
- TRPM3-related Intellectual Disability and Epilepsy (1 variants)
- Intellectual disability (1 variants)
- Seizure;Global developmental delay (1 variants)
- Familial progressive retinal dystrophy-iris coloboma-congenital cataract syndrome (1 variants)
- TRPM3 related disorder (1 variants)
- Seizure (1 variants)
- Autosomal dominant non-syndromic intellectual disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPM3 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 | 8 | |||||
missense | 88 | 103 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region ? | 1 | 1 | 1 | 3 | ||
non coding ? | 11 | 14 | ||||
Total | 1 | 6 | 103 | 9 | 10 |
Variants in TRPM3
This is a list of pathogenic ClinVar variants found in the TRPM3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-70535990-G-A | Uncertain significance (Nov 14, 2022) | |||
9-70536026-C-T | Intellectual disability;Epileptic encephalopathy | Uncertain significance (Nov 30, 2021) | ||
9-70536043-G-C | TRPM3-related disorder | Likely benign (Jun 11, 2019) | ||
9-70536068-C-T | Benign (Sep 25, 2020) | |||
9-70536086-C-T | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) | ||
9-70536087-G-A | Inborn genetic diseases | Uncertain significance (May 09, 2023) | ||
9-70536108-T-G | Uncertain significance (May 15, 2020) | |||
9-70536143-G-A | TRPM3-related disorder | Benign/Likely benign (May 01, 2022) | ||
9-70536143-G-T | Inborn genetic diseases | Uncertain significance (Dec 07, 2023) | ||
9-70536170-T-C | Inborn genetic diseases | Uncertain significance (Feb 22, 2023) | ||
9-70536175-G-A | TRPM3-related disorder | Likely benign (Mar 12, 2019) | ||
9-70536191-A-C | Inborn genetic diseases | Uncertain significance (Nov 06, 2023) | ||
9-70536194-G-A | TRPM3-related disorder | Benign (Apr 04, 2019) | ||
9-70536200-T-C | Likely pathogenic (Oct 08, 2021) | |||
9-70536224-T-A | TRPM3-related disorder | Benign (Feb 19, 2019) | ||
9-70536251-A-G | Inborn genetic diseases | Uncertain significance (Feb 14, 2023) | ||
9-70536345-C-A | Inborn genetic diseases | Uncertain significance (Mar 01, 2024) | ||
9-70536415-C-A | Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures | Uncertain significance (Dec 19, 2023) | ||
9-70536426-T-C | Inborn genetic diseases | Uncertain significance (Feb 05, 2024) | ||
9-70536428-C-T | Developmental disorder | Likely benign (Jan 06, 2022) | ||
9-70536471-C-T | TRPM3-related disorder | Likely benign (Apr 01, 2024) | ||
9-70536476-T-C | Uncertain significance (Jan 02, 2020) | |||
9-70536546-G-C | Inborn genetic diseases | Uncertain significance (Nov 03, 2023) | ||
9-70536569-C-T | Inborn genetic diseases | Uncertain significance (Nov 28, 2023) | ||
9-70536620-C-G | Neurodevelopmental disorder | Uncertain significance (Jun 24, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TRPM3 | protein_coding | protein_coding | ENST00000377110 | 25 | 917842 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.69e-7 | 1.00 | 125670 | 0 | 78 | 125748 | 0.000310 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.18 | 716 | 998 | 0.717 | 0.0000576 | 11294 |
Missense in Polyphen | 289 | 471.78 | 0.61257 | 5303 | ||
Synonymous | 0.133 | 374 | 377 | 0.991 | 0.0000230 | 3243 |
Loss of Function | 5.64 | 27 | 82.2 | 0.329 | 0.00000471 | 917 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000695 | 0.000695 |
Ashkenazi Jewish | 0.000710 | 0.000695 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000278 | 0.000277 |
European (Non-Finnish) | 0.000328 | 0.000325 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000370 | 0.000359 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium channel mediating constitutive calcium ion entry. Its activity is increased by reduction in extracellular osmolarity, by store depletion and muscarinic receptor activation. {ECO:0000269|PubMed:12672799, ECO:0000269|PubMed:12672827}.;
- Pathway
- Stimuli-sensing channels;Ion channel transport;Transport of small molecules;TRP channels
(Consensus)
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- loftool
- 0.767
- rvis_EVS
- -1.09
- rvis_percentile_EVS
- 6.98
Haploinsufficiency Scores
- pHI
- 0.476
- hipred
- Y
- hipred_score
- 0.747
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0628
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Trpm3
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);
Gene ontology
- Biological process
- cation transport;detection of temperature stimulus;sensory perception of temperature stimulus;protein tetramerization;calcium ion transmembrane transport
- Cellular component
- plasma membrane;integral component of membrane
- Molecular function
- calcium activated cation channel activity;cation channel activity;calcium channel activity