PCBP4

poly(rC) binding protein 4

Basic information

Region (hg38): 3:51957454-51974016

Links

ENSG00000090097 ∙ NCBI:57060 ∙ OMIM:608503 ∙ HGNC:8652 ∙ Uniprot:P57723 ∙ 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 PCBP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCBP4 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in PCBP4

This is a list of pathogenic ClinVar variants found in the PCBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-51958108-C-T		not specified	Uncertain significance (Jun 14, 2023)
3-51958125-G-A		not specified	Uncertain significance (Sep 06, 2022)
3-51958140-C-G		not specified	Uncertain significance (Jun 16, 2024)
3-51958159-A-C			Likely benign (May 31, 2018)
3-51958195-G-A		not specified	Uncertain significance (May 26, 2024)
3-51958228-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-51958234-C-T		not specified	Uncertain significance (Aug 12, 2022)
3-51958258-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-51958806-A-G		not specified	Uncertain significance (Nov 17, 2022)
3-51958808-T-A		not specified	Uncertain significance (Sep 17, 2021)
3-51958869-C-T		not specified	Uncertain significance (Jun 19, 2024)
3-51958937-C-T		not specified	Uncertain significance (Feb 27, 2023)
3-51959261-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-51959291-A-C		not specified	Uncertain significance (Jan 19, 2024)
3-51959391-C-A		not specified	Uncertain significance (Nov 15, 2021)
3-51959908-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-51959959-G-A		not specified	Uncertain significance (Sep 22, 2023)
3-51960269-T-C		not specified	Uncertain significance (Dec 14, 2023)
3-51960279-C-G		not specified	Uncertain significance (Jun 11, 2021)
3-51960290-T-C		not specified	Uncertain significance (Oct 05, 2023)
3-51960582-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-51960599-C-T		not specified	Uncertain significance (May 15, 2024)
3-51960606-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-51960626-G-T		not specified	Uncertain significance (Oct 17, 2023)
3-51961179-C-T		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCBP4	protein_coding	protein_coding	ENST00000461554	12	10957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00237	0.995	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	175	248	0.705	0.0000154	2543
Missense in Polyphen		71	118.35	0.59991		1162
Synonymous	0.0551	108	109	0.993	0.00000738	901
Loss of Function	2.58	8	20.7	0.387	0.00000114	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000191	0.000185
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000362	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. {ECO:0000250}.
• Pathway: TP53 Regulates Transcription of Cell Cycle Genes;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional activation of cell cycle inhibitor p21 ;Transcriptional activation of p53 responsive genes ;p53-Dependent G1 DNA Damage Response;p53-Dependent G1/S DNA damage checkpoint;G1/S DNA Damage Checkpoints;Cell Cycle Checkpoints;TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Direct p53 effectors;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.728
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.282
• hipred: N
• hipred_score: 0.403
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.756

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcbp4
• Phenotype: renal/urinary system phenotype; respiratory system phenotype; neoplasm; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;regulation of mRNA stability
• Cellular component: cytosol
• Molecular function: DNA binding;RNA binding;mRNA 3'-UTR binding