PTBP3

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

Basic information

Region (hg38): 9:112217715-112333664

Previous symbols: [ "ROD1" ]

Links

ENSG00000119314 ∙ NCBI:9991 ∙ OMIM:607527 ∙ HGNC:10253 ∙ Uniprot:O95758 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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
9-112223964-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)
9-112234888-C-G		not specified	Uncertain significance (Nov 09, 2021)
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)
9-112268105-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)
9-112268162-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)
9-112275954-C-T		not specified	Uncertain significance (Aug 22, 2023)
9-112275957-G-A		not specified	Uncertain significance (Jan 09, 2024)
9-112275983-C-T		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

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: 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

• 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

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