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GeneBe

PTBP3

polypyrimidine tract binding protein 3, the group of RNA binding motif containing

Basic information

Region (hg38): 9:112217715-112333664

Previous symbols: [ "ROD1" ]

Links

ENSG00000119314NCBI:9991OMIM:607527HGNC:10253Uniprot:O95758AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTBP3 gene.

  • Inborn genetic diseases (19 variants)

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
19
clinvar
19
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 19 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
9-112223964-G-A not specified Uncertain significance (Oct 06, 2021)2253385
9-112227501-T-C not specified Uncertain significance (Jun 28, 2022)3220573
9-112228397-G-A not specified Uncertain significance (Jun 02, 2023)2555982
9-112232116-T-A not specified Uncertain significance (Jan 16, 2024)2352734
9-112232136-C-T not specified Uncertain significance (Jul 19, 2023)2597907
9-112234888-C-G not specified Uncertain significance (Nov 09, 2021)2364577
9-112250944-T-C not specified Uncertain significance (Nov 18, 2022)2219578
9-112251037-T-C not specified Uncertain significance (Mar 01, 2023)2491974
9-112251091-G-T not specified Uncertain significance (Jan 09, 2024)3220576
9-112262511-A-G not specified Uncertain significance (Oct 30, 2023)3220575
9-112262523-T-C not specified Uncertain significance (Jul 12, 2023)2611372
9-112262526-T-C not specified Uncertain significance (Apr 06, 2022)2366699
9-112262548-C-T not specified Uncertain significance (Dec 12, 2022)2328376
9-112268052-T-G not specified Uncertain significance (Oct 05, 2021)2253041
9-112268105-A-G not specified Uncertain significance (Nov 22, 2021)2262114
9-112268119-C-T not specified Uncertain significance (Apr 19, 2023)2521212
9-112268150-T-C not specified Uncertain significance (Dec 17, 2021)2268030
9-112268162-C-T not specified Uncertain significance (Nov 01, 2022)2402296
9-112275912-C-T not specified Uncertain significance (Dec 05, 2022)2332657
9-112275953-A-C not specified Uncertain significance (May 11, 2022)2404908
9-112275954-C-T not specified Uncertain significance (Aug 22, 2023)2621138
9-112275957-G-A not specified Uncertain significance (Jan 09, 2024)3220574
9-112275983-C-T not specified Uncertain significance (Apr 25, 2023)2540378

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PTBP3protein_codingprotein_codingENST00000458258 14115233
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8630.1371257230231257460.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.202423010.8050.00001533621
Missense in Polyphen3052.6750.56953723
Synonymous0.1841031050.9770.000005391130
Loss of Function4.08528.50.1750.00000181311

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004630.000462
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.0001410.000139
European (Non-Finnish)0.00007090.0000703
Middle Eastern0.000.00
South Asian0.000.00
Other0.0004940.000489

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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