PCBP4

protein-coding

poly(rC) binding protein 4

Gene summary

This gene encodes a member of the KH-domain protein subfamily. Proteins of this subfamily, also referred to as alpha-CPs, bind to RNA with a specificity for C-rich pyrimidine regions. Alpha-CPs play important roles in post-transcriptional activities and have different cellular distributions. This gene is induced by the p53 tumor suppressor, and the encoded protein can suppress cell proliferation by inducing apoptosis and cell cycle arrest in G(2)-M. This gene's protein is found in the cytoplasm, yet it lacks the nuclear localization signals found in other subfamily members. Multiple alternatively spliced transcript variants have been described, but the full-length nature for only some has been determined. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001174100.2

Inheritance

—

ClinVar variants

U:57B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr3:51,957,454-51,974,016

External References & Databases

Ensembl (ENSG00000090097)

Transcript & Mutation Effects

hg38 • Region Span ~16.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCBP4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001174100.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			52 clinvar	3 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	57	4	0	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 227 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001174100.2	RefSeq	NP_001167571.1	12	MANE Select
ENST00000461554.6	Ensembl	ENSP00000417196.1	12	MANE Select
NM_001363885.1	RefSeq	NP_001350814.1	12	Standard
NM_020418.4	RefSeq	NP_065151.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TP53 Regulates Transcription of Cell Cycle Genes
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
Transcriptional activation of cell cycle inhibitor p21

Biological Process

DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
regulation of mRNA stability

Molecular Function

DNA binding
RNA binding
mRNA 3'-UTR binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000461554
Coding exons: 12
Length: 10957
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.65	175	248	0.705	0.0000154	2543
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.00036	0.00036	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.728
RVIS EVS: -0.14
RVIS percentile EVS: 43.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.756

Gene Damage Prediction

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