PTBP3
Basic information
Region (hg38): 9:112217715-112333664
Previous symbols: [ "ROD1" ]
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 PTBP3 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 | 23 | 23 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 23 | 0 | 0 |
Variants in PTBP3
This is a list of pathogenic ClinVar variants found in the PTBP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-112223951-C-T | not specified | Uncertain significance (May 15, 2024) | ||
9-112223964-G-A | not specified | Uncertain significance (Oct 06, 2021) | ||
9-112227501-T-C | not specified | Uncertain significance (Jun 28, 2022) | ||
9-112228397-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
9-112232116-T-A | not specified | Uncertain significance (Jan 16, 2024) | ||
9-112232136-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
9-112234844-C-T | not specified | Uncertain significance (Apr 27, 2024) | ||
9-112234877-A-G | not specified | Uncertain significance (May 20, 2024) | ||
9-112234888-C-G | not specified | Uncertain significance (Apr 26, 2024) | ||
9-112250944-T-C | not specified | Uncertain significance (Nov 18, 2022) | ||
9-112251037-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
9-112251091-G-T | not specified | Uncertain significance (Jan 09, 2024) | ||
9-112262511-A-G | not specified | Uncertain significance (Oct 30, 2023) | ||
9-112262523-T-C | not specified | Uncertain significance (Jul 12, 2023) | ||
9-112262526-T-C | not specified | Uncertain significance (Apr 06, 2022) | ||
9-112262548-C-T | not specified | Uncertain significance (Dec 12, 2022) | ||
9-112268052-T-G | not specified | Uncertain significance (Oct 05, 2021) | ||
9-112268089-T-C | not specified | Uncertain significance (Jun 10, 2024) | ||
9-112268105-A-G | not specified | Uncertain significance (Nov 22, 2021) | ||
9-112268119-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
9-112268150-T-C | not specified | Uncertain significance (Dec 17, 2021) | ||
9-112268161-A-G | not specified | Uncertain significance (May 09, 2024) | ||
9-112268162-C-T | not specified | Uncertain significance (Nov 01, 2022) | ||
9-112275912-C-T | not specified | Uncertain significance (Dec 05, 2022) | ||
9-112275953-A-C | not specified | Uncertain significance (May 11, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PTBP3 | protein_coding | protein_coding | ENST00000458258 | 14 | 115233 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.863 | 0.137 | 125723 | 0 | 23 | 125746 | 0.0000915 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.20 | 242 | 301 | 0.805 | 0.0000153 | 3621 |
Missense in Polyphen | 30 | 52.675 | 0.56953 | 723 | ||
Synonymous | 0.184 | 103 | 105 | 0.977 | 0.00000539 | 1130 |
Loss of Function | 4.08 | 5 | 28.5 | 0.175 | 0.00000181 | 311 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000463 | 0.000462 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000141 | 0.000139 |
European (Non-Finnish) | 0.0000709 | 0.0000703 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.000494 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding protein that mediates pre-mRNA alternative splicing regulation. Plays a role in the regulation of cell proliferation, differentiation and migration. Positive regulator of EPO-dependent erythropoiesis. Participates in cell differentiation regulation by repressing tissue-specific exons. Promotes FAS exon 6 skipping. Binds RNA, preferentially to both poly(G) and poly(U). {ECO:0000269|PubMed:10207106, ECO:0000269|PubMed:18335065, ECO:0000269|PubMed:19441079, ECO:0000269|PubMed:20937273}.;
Recessive Scores
- pRec
- 0.0949
Intolerance Scores
- loftool
- rvis_EVS
- -0.62
- rvis_percentile_EVS
- 17.16
Haploinsufficiency Scores
- pHI
- 0.960
- hipred
- Y
- hipred_score
- 0.591
- ghis
- 0.634
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptbp3
- Phenotype
Gene ontology
- Biological process
- mRNA processing;RNA splicing;anatomical structure morphogenesis;negative regulation of RNA splicing;erythrocyte maturation;regulation of cell differentiation
- Cellular component
- nucleus
- Molecular function
- RNA binding