PTMA
Basic information
Region (hg38): 2:231706894-231713551
Previous symbols: [ "TMSA" ]
Links
Phenotypes
GenCC
Source:
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 PTMA 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in PTMA
This is a list of pathogenic ClinVar variants found in the PTMA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-231708739-A-C | not specified | Uncertain significance (Feb 23, 2023) | ||
| 2-231711387-A-G | not specified | Uncertain significance (Apr 13, 2022) | ||
| 2-231711394-G-C | not specified | Uncertain significance (Jul 06, 2021) | ||
| 2-231711931-C-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 2-231712837-G-A | not specified | Uncertain significance (May 11, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTMA | protein_coding | protein_coding | ENST00000341369 | 5 | 6647 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0345 | 0.837 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.258 | 52 | 57.5 | 0.904 | 0.00000287 | 738 |
| Missense in Polyphen | 1 | 3.791 | 0.26379 | 47 | ||
| Synonymous | -1.18 | 26 | 19.4 | 1.34 | 9.88e-7 | 162 |
| Loss of Function | 1.20 | 3 | 6.25 | 0.480 | 2.64e-7 | 91 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Prothymosin alpha may mediate immune function by conferring resistance to certain opportunistic infections.;
- Pathway
- Epstein-Barr virus infection - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Validated targets of C-MYC transcriptional activation
(Consensus)
Intolerance Scores
- loftool
- 0.212
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.460
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.996
Mouse Genome Informatics
- Gene name
- Ptma
- 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);
Zebrafish Information Network
- Gene name
- ptmab
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- curved
Gene ontology
- Biological process
- transcription, DNA-templated;histone exchange
- Cellular component
- nucleus;nucleoplasm;cytosol
- Molecular function
- protein binding;activating transcription factor binding;histone binding