PCBP3

poly(rC) binding protein 3

Basic information

Region (hg38): 21:45643693-45942454

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.

• Inborn genetic diseases (9 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.

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						0
non coding						0
Total	0	0	9	0	2

Variants in PCBP3

This is a list of pathogenic ClinVar variants found in the PCBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-45896212-C-T		PCBP3-related disorder	Benign (Jan 02, 2020)
21-45896355-A-C		not specified	Uncertain significance (Jul 14, 2021)
21-45899581-AT-A		PCBP3-related disorder	Likely benign (Nov 25, 2019)
21-45899581-A-AT		PCBP3-related disorder	Likely benign (Nov 04, 2019)
21-45901090-A-G		not specified	Uncertain significance (Dec 17, 2023)
21-45909438-T-C		PCBP3-related disorder	Benign (Oct 29, 2019)
21-45910952-G-A		PCBP3-related disorder	Likely benign (Apr 06, 2022)
21-45910957-G-A		not specified	Uncertain significance (Jun 05, 2023)
21-45911001-G-A		not specified	Uncertain significance (Jun 07, 2023)
21-45913957-C-T		not specified	Uncertain significance (Feb 17, 2024)
21-45913981-C-T		not specified	Uncertain significance (Aug 13, 2021)
21-45914500-C-T		PCBP3-related disorder	Benign (Oct 30, 2019)
21-45917570-GTC-G		PCBP3-related disorder	Likely benign (Nov 04, 2019)
21-45930793-G-A		PCBP3-related disorder	Likely benign (Nov 25, 2019)
21-45930804-A-G		not specified	Uncertain significance (Nov 08, 2022)
21-45930812-G-A		not specified	Uncertain significance (Mar 01, 2024)
21-45935260-C-A		not specified	Uncertain significance (Nov 22, 2022)
21-45935267-C-T		not specified	Uncertain significance (Jun 06, 2023)
21-45941676-G-A		PCBP3-related disorder	Benign (Nov 25, 2019)
21-45941689-G-A		not specified	Uncertain significance (Aug 01, 2022)
21-45941694-G-A		not specified	Uncertain significance (Dec 07, 2021)

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