TMEM30A
transmembrane protein 30A
Basic information
Region (hg38): 6:75252924-75284948
Previous symbols: [ "C6orf67" ]
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 TMEM30A 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in TMEM30A
This is a list of pathogenic ClinVar variants found in the TMEM30A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-75259353-A-G | not specified | Uncertain significance (Jan 20, 2023) | ||
| 6-75260845-T-C | not specified | Uncertain significance (Dec 14, 2023) | ||
| 6-75260883-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 6-75265242-T-C | not specified | Uncertain significance (Jul 12, 2023) | ||
| 6-75267699-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
| 6-75284577-C-G | not specified | Uncertain significance (Mar 19, 2024) | ||
| 6-75284577-C-T | not specified | Uncertain significance (May 26, 2022) | ||
| 6-75284580-C-G | not specified | Uncertain significance (Apr 29, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMEM30A | protein_coding | protein_coding | ENST00000230461 | 7 | 32045 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00319 | 0.987 | 125730 | 0 | 18 | 125748 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.06 | 165 | 208 | 0.794 | 0.0000108 | 2382 |
| Missense in Polyphen | 43 | 80.743 | 0.53255 | 961 | ||
| Synonymous | 0.269 | 70 | 72.9 | 0.960 | 0.00000368 | 697 |
| Loss of Function | 2.26 | 7 | 17.1 | 0.410 | 0.00000103 | 199 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000214 | 0.000213 |
| Ashkenazi Jewish | 0.000100 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000806 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000981 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Accessory component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules. The beta subunit may assist in binding of the phospholipid substrate. Required for the proper folding, assembly and ER to Golgi exit of the ATP8A2:TMEM30A flippase complex. ATP8A2:TMEM30A may be involved in regulation of neurite outgrowth, and, reconstituted to liposomes, predomiminantly transports phosphatidylserine (PS) and to a lesser extent phosphatidylethanolamine (PE). The ATP8A1:TMEM30A flippase complex seems to play a role in regulation of cell migration probably involving flippase-mediated translocation of phosphatidylethanolamine (PE) at the plasma membrane. Required for the formation of the ATP8A2, ATP8B1 and ATP8B2 P-type ATPAse intermediate phosphoenzymes. Involved in uptake of platelet- activating factor (PAF), synthetic drug alkylphospholipid edelfosine, and, probably in association with ATP8B1, of perifosine. Also mediate the export of alpha subunits ATP8A1, ATP8B1, ATP8B2, ATP8B4, ATP10A, ATP10B, ATP10D, ATP11A, ATP11B and ATP11C from the ER to other membrane localizations. {ECO:0000269|PubMed:20510206, ECO:0000269|PubMed:20947505, ECO:0000269|PubMed:20961850, ECO:0000269|PubMed:21289302}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- loftool
- 0.341
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.211
- hipred
- Y
- hipred_score
- 0.639
- ghis
- 0.649
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.540
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmem30a
- Phenotype
- immune system phenotype; skeleton phenotype; liver/biliary system 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); growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- drug transmembrane transport;positive regulation of neuron projection development;aminophospholipid transport;protein localization to endosome;neutrophil degranulation;phospholipid translocation;positive regulation of protein exit from endoplasmic reticulum
- Cellular component
- endoplasmic reticulum;Golgi apparatus;plasma membrane;membrane;integral component of membrane;apical plasma membrane;transport vesicle membrane;azurophil granule membrane;specific granule membrane
- Molecular function
- phospholipid-translocating ATPase activity;protein binding;aminophospholipid transmembrane transporter activity