PCBP1

poly(rC) binding protein 1, the group of Heterogeneous nuclear ribonucleoproteins

Basic information

Region (hg38): 2:70087477-70089203

Links

ENSG00000169564

∙ NCBI:5093 ∙ OMIM:601209 ∙ HGNC:8647 ∙ Uniprot:Q15365 ∙ 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 PCBP1 gene.

not_specified (14 variants)
Neurodevelopmental_disorder (1 variants)
Inborn_genetic_diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006196.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar			15
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	15	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCBP1	protein_coding	protein_coding	ENST00000303577	1	1748

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.909	0.0899	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.20	74	202	0.367	0.00000923	2326
Missense in Polyphen		9	56.099	0.16043		696
Synonymous	-5.05	142	83.3	1.70	0.00000404	763
Loss of Function	2.58	0	7.74	0.00	3.34e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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. In case of infection by poliovirus, plays a role in initiation of viral RNA replication in concert with the viral protein 3CD (PubMed:12414943). {ECO:0000269|PubMed:12414943}.;
Pathway: Spliceosome - Homo sapiens (human);Ferroptosis - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

loftool
rvis_EVS: -0.32
rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

pHI: 0.450
hipred: Y
hipred_score: 0.734
ghis: 0.587

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pcbp1
Phenotype: growth/size/body region phenotype; 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);

Gene ontology

Biological process: mRNA splicing, via spliceosome;RNA metabolic process;viral RNA genome replication;positive regulation of transcription by RNA polymerase II
Cellular component: nucleoplasm;cytoplasm;cytosol;membrane;nuclear speck;cytoplasmic ribonucleoprotein granule;extracellular exosome
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;single-stranded DNA binding;RNA binding;mRNA binding;protein binding;cadherin binding;sequence-specific single stranded DNA binding