TMEM63B
Basic information
Region (hg38): 6:44126914-44155519
Previous symbols: [ "C6orf110" ]
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Strong), mode of inheritance: AD
- TMEM63B-related developmental and epileptic encephalopathy with anemia (Moderate), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (61 variants)
- not_provided (30 variants)
- DEVELOPMENTAL_AND_EPILEPTIC_ENCEPHALOPATHY_118 (4 variants)
- not_specified (2 variants)
- Rare_epilepsy (1 variants)
- TMEM63B-related_condition (1 variants)
- TMEM63B-related_Neurodevelopmental_disorder (1 variants)
- TMEM63B-associated_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM63B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018426.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 75 | 86 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 4 | 3 | 79 | 5 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMEM63B | protein_coding | protein_coding | ENST00000259746 | 23 | 28606 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000821 | 125735 | 0 | 8 | 125743 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.22 | 243 | 511 | 0.475 | 0.0000309 | 5448 |
| Missense in Polyphen | 56 | 193.94 | 0.28874 | 2065 | ||
| Synonymous | -1.14 | 234 | 213 | 1.10 | 0.0000136 | 1635 |
| Loss of Function | 5.88 | 3 | 46.1 | 0.0651 | 0.00000231 | 525 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000542 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as an osmosensitive calcium-permeable cation channel. {ECO:0000250}.;
- Pathway
- Fibroblast growth factor-1
(Consensus)
Intolerance Scores
- loftool
- 0.0706
- rvis_EVS
- -1.11
- rvis_percentile_EVS
- 6.78
Haploinsufficiency Scores
- pHI
- 0.283
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.519
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmem63b
- Phenotype
- vision/eye 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- ion transmembrane transport
- Cellular component
- plasma membrane;actin cytoskeleton;integral component of membrane
- Molecular function
- calcium activated cation channel activity