PTBP2

polypyrimidine tract binding protein 2, the group of Heterogeneous nuclear ribonucleoproteins|RNA binding motif containing

Basic information

Region (hg38): 1:96721665-96823738

Links

ENSG00000117569 ∙ NCBI:58155 ∙ OMIM:608449 ∙ HGNC:17662 ∙ Uniprot:Q9UKA9 ∙ 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 PTBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTBP2 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					2	2
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	9	1	2

Variants in PTBP2

This is a list of pathogenic ClinVar variants found in the PTBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-96721870-C-A		not specified	Uncertain significance (Jul 11, 2023)
1-96749651-A-T		not specified	Likely benign (Oct 27, 2020)
1-96751419-T-C			Benign (Oct 10, 2018)
1-96751477-A-C		not specified	Uncertain significance (Jun 06, 2023)
1-96769734-A-G			Benign (Jun 20, 2018)
1-96769750-G-T		not specified	Uncertain significance (Dec 01, 2022)
1-96770784-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-96770795-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-96777630-A-G		not specified	Uncertain significance (May 10, 2022)
1-96785115-C-T			Benign (Aug 02, 2017)
1-96785224-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-96804812-C-G		not specified	Uncertain significance (May 14, 2024)
1-96804872-G-A		not specified	Uncertain significance (Jun 02, 2023)
1-96806905-A-G		not specified	Uncertain significance (Jun 11, 2024)
1-96812716-G-A		not specified	Uncertain significance (Sep 22, 2021)
1-96812927-C-G		not specified	Uncertain significance (Jun 17, 2024)
1-96813340-C-G		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTBP2	protein_coding	protein_coding	ENST00000426398	14	102074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00117	125186	0	2	125188	0.00000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.20	134	287	0.468	0.0000145	3481
Missense in Polyphen		32	121.23	0.26395		1499
Synonymous	0.172	97	99.2	0.978	0.00000505	1053
Loss of Function	4.59	2	28.4	0.0704	0.00000168	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000882
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein which binds to intronic polypyrimidine tracts and mediates negative regulation of exons splicing. May antagonize in a tissue-specific manner the ability of NOVA1 to activate exon selection. In addition to its function in pre-mRNA splicing, plays also a role in the regulation of translation. Isoform 5 has a reduced affinity for RNA. {ECO:0000269|PubMed:11003644, ECO:0000269|PubMed:12667457}.
• Pathway: TarBasePathway;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;mRNA Processing;internal ribosome entry pathway (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.290
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.848
• hipred: Y
• hipred_score: 0.816
• ghis: 0.666

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.696

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptbp2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular 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); 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: mRNA splice site selection;spinal cord development;cerebellum development;negative regulation of RNA splicing;regulation of neural precursor cell proliferation
• Cellular component: spliceosomal complex;growth cone;neuronal cell body
• Molecular function: RNA binding;mRNA binding