TMEM100
transmembrane protein 100
Basic information
Region (hg38): 17:55719626-55732121
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM100 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 | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in TMEM100
This is a list of pathogenic ClinVar variants found in the TMEM100 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-55720679-C-T | not specified | Uncertain significance (Mar 04, 2024) | ||
| 17-55720695-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
| 17-55720704-T-C | not specified | Uncertain significance (Jan 08, 2024) | ||
| 17-55720734-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
| 17-55720779-A-G | not specified | Uncertain significance (May 06, 2024) | ||
| 17-55720809-A-C | not specified | Uncertain significance (Aug 08, 2023) | ||
| 17-55720853-G-A | not specified | Uncertain significance (Jul 25, 2023) | ||
| 17-55720854-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 17-55720902-T-C | not specified | Uncertain significance (Jan 04, 2024) | ||
| 17-55720965-G-C | not specified | Uncertain significance (Jan 26, 2022) | ||
| 17-55721015-G-A | not specified | Likely benign (May 26, 2024) | ||
| 17-55721027-G-A | not specified | Uncertain significance (Mar 06, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMEM100 | protein_coding | protein_coding | ENST00000575734 | 1 | 12495 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.534 | 0.412 | 125702 | 0 | 3 | 125705 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.793 | 60 | 80.0 | 0.750 | 0.00000455 | 867 |
| Missense in Polyphen | 26 | 37.171 | 0.69947 | 415 | ||
| Synonymous | 0.876 | 27 | 33.4 | 0.807 | 0.00000213 | 288 |
| Loss of Function | 1.39 | 0 | 2.25 | 0.00 | 9.27e-8 | 34 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role during embryonic arterial endothelium differentiation and vascular morphogenesis through the ACVRL1 receptor-dependent signaling pathway upon stimulation by bone morphogenetic proteins, such as GDF2/BMP9 and BMP10. Involved in the regulation of nociception, acting as a modulator of the interaction between TRPA1 and TRPV1, two molecular sensors and mediators of pain signals in dorsal root ganglia (DRG) neurons. Mechanistically, it weakens their interaction, thereby releasing the inhibition of TRPA1 by TRPV1 and increasing the single-channel open probability of the TRPA1-TRPV1 complex. {ECO:0000250|UniProtKB:Q9CQG9}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- 0.124
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.108
- hipred
- N
- hipred_score
- 0.310
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmem100
- Phenotype
- immune system 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); normal 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); hematopoietic system phenotype; 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); 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
- angiogenesis;vasculogenesis;in utero embryonic development;epithelial to mesenchymal transition involved in endocardial cushion formation;Notch signaling pathway;BMP signaling pathway;protein kinase B signaling;positive regulation of endothelial cell differentiation;regulation of calcium-mediated signaling;regulation of sensory perception of pain;arterial endothelial cell differentiation;cellular response to BMP stimulus;positive regulation of vasculogenesis
- Cellular component
- endoplasmic reticulum;plasma membrane;integral component of membrane;perikaryon;perinuclear region of cytoplasm
- Molecular function
- molecular_function;protein binding