PCBP3

poly(rC) binding protein 3

Basic information

Region (hg38): 21:45643694-45942454

Previous symbols: [ "PCBP3-OT1", "PCBP3OT" ]

Links

ENSG00000183570 ∙ NCBI:54039 ∙ OMIM:608502 ∙ HGNC:8651 ∙ Uniprot:P57721 ∙ 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 PCBP3 gene.

• not_specified (31 variants)
• PCBP3-related_disorder (7 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCBP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001384156.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	2	4
missense			31			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	2	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCBP3	protein_coding	protein_coding	ENST00000400314	14	298761

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.843	0.157	124781	0	7	124788	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	144	230	0.626	0.0000132	2407
Missense in Polyphen		26	61.42	0.42331		664
Synonymous	0.861	80	90.4	0.885	0.00000599	739
Loss of Function	3.75	4	23.7	0.169	0.00000116	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. {ECO:0000250}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.418
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.745
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.949

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcbp3

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;mRNA metabolic process
• Cellular component: nucleus;cytosol;extracellular exosome
• Molecular function: DNA-binding transcription repressor activity, RNA polymerase II-specific;double-stranded DNA binding;RNA binding;C-rich single-stranded DNA binding