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.

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.

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			3			3
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	3	0	0

Variants in PCBP1

This is a list of pathogenic ClinVar variants found in the PCBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-70087777-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-70087880-G-A		Neurodevelopmental disorder	Uncertain significance (Sep 21, 2021)
2-70087976-A-G		not specified	Uncertain significance (Sep 20, 2024)
2-70088017-G-T		not specified	Uncertain significance (Jul 02, 2024)
2-70088293-C-T		Inborn genetic diseases	Likely pathogenic (Jun 17, 2014)
2-70088392-C-A		not specified	Uncertain significance (Apr 07, 2023)
2-70088396-C-T		not specified	Uncertain significance (May 12, 2024)
2-70088429-C-G		not specified	Uncertain significance (Nov 23, 2024)
2-70088431-A-G		not specified	Uncertain significance (Apr 08, 2024)

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

• 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