PTBP1

polypyrimidine tract binding protein 1, the group of MicroRNA protein coding host genes|RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins

Basic information

Region (hg38): 19:797075-812327

Previous symbols: [ "PTB" ]

Links

ENSG00000011304 ∙ NCBI:5725 ∙ OMIM:600693 ∙ HGNC:9583 ∙ Uniprot:P26599 ∙ 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 PTBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTBP1 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				9	6	15
missense			17	2		19
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding			1		2	3
Total	0	0	19	11	8

Variants in PTBP1

This is a list of pathogenic ClinVar variants found in the PTBP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-797498-A-G			Uncertain significance (-)
19-797499-T-C			Uncertain significance (Aug 08, 2019)
19-797517-G-C			Benign (Oct 20, 2021)
19-803603-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-803609-A-G		not specified	Uncertain significance (Feb 22, 2023)
19-803611-C-G		not specified	Uncertain significance (Apr 01, 2024)
19-803625-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-804095-A-G		not specified	Uncertain significance (Dec 19, 2023)
19-804184-C-T			Benign/Likely benign (Jan 01, 2023)
19-804366-G-A			Likely benign (Mar 30, 2018)
19-804442-C-T			Likely benign (Jun 13, 2018)
19-804542-C-T		not specified	Uncertain significance (May 25, 2022)
19-804560-A-G		not specified	Uncertain significance (Oct 27, 2022)
19-804601-G-C		not specified	Uncertain significance (Jun 05, 2024)
19-804602-C-T		not specified	Uncertain significance (May 31, 2023)
19-804606-C-T			Likely benign (Mar 30, 2018)
19-804608-T-C		not specified	Uncertain significance (May 18, 2023)
19-804613-G-A			Likely benign (Apr 24, 2018)
19-804621-G-A		not specified	Uncertain significance (Jun 09, 2022)
19-804660-G-A			Likely benign (Jul 06, 2018)
19-804916-G-C		not specified	Uncertain significance (Jan 03, 2022)
19-804921-C-T			Benign (Jun 08, 2017)
19-805006-C-T			Likely benign (Mar 30, 2018)
19-805051-G-T			Likely benign (Jul 20, 2018)
19-805056-G-T		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTBP1	protein_coding	protein_coding	ENST00000356948	15	15253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000393	125733	0	3	125736	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	276	365	0.757	0.0000246	3627
Missense in Polyphen		19	68.021	0.27933		867
Synonymous	-4.97	247	166	1.49	0.0000130	1105
Loss of Function	4.63	1	26.9	0.0371	0.00000134	299

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	0.0000464	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in pre-mRNA splicing and in the regulation of alternative splicing events. Activates exon skipping of its own pre-mRNA during muscle cell differentiation. Binds to the polypyrimidine tract of introns. May promote RNA looping when bound to two separate polypyrimidine tracts in the same pre-mRNA. May promote the binding of U2 snRNP to pre-mRNA. Cooperates with RAVER1 to modulate switching between mutually exclusive exons during maturation of the TPM1 pre-mRNA. Represses the splicing of MAPT/Tau exon 10 (PubMed:15009664). In case of infection by picornaviruses, binds to the viral internal ribosome entry site (IRES) and stimulates the IRES-mediated translation (PubMed:21518806). {ECO:0000269|PubMed:11003644, ECO:0000269|PubMed:15009664, ECO:0000269|PubMed:16179478, ECO:0000269|PubMed:16260624, ECO:0000269|PubMed:21518792, ECO:0000269|PubMed:21518806}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;mir-124 predicted interactions with cell cycle and differentiation;mRNA Processing;FGFR2 alternative splicing;Signaling by FGFR2;Signal Transduction;Signaling by FGFR;internal ribosome entry pathway;Metabolism of RNA;mRNA Splicing - Major Pathway;Signaling by Receptor Tyrosine Kinases;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.248

Intolerance Scores

• loftool: 0.184
• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.64

Haploinsufficiency Scores

• pHI: 0.888
• hipred: Y
• hipred_score: 0.783
• ghis: 0.661

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ptbp1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; embryo 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); growth/size/body region phenotype; craniofacial phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ptbp1a
• Affected structure: mid intestine epithelium
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;mRNA processing;RNA splicing;fibroblast growth factor receptor signaling pathway;RNA metabolic process;negative regulation of RNA splicing;positive regulation of protein dephosphorylation;negative regulation of mRNA splicing, via spliceosome;negative regulation of muscle cell differentiation;positive regulation of calcineurin-NFAT signaling cascade;IRES-dependent viral translational initiation
• Cellular component: nucleoplasm;nucleolus;membrane;extracellular exosome
• Molecular function: RNA binding;protein binding;poly-pyrimidine tract binding;pre-mRNA binding