PAPOLA

poly(A) polymerase alpha

Basic information

Region (hg38): 14:96501433-96567116

Links

ENSG00000090060 ∙ NCBI:10914 ∙ OMIM:605553 ∙ HGNC:14981 ∙ Uniprot:P51003 ∙ 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 PAPOLA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAPOLA 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				1	3	4
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	26	3	3

Variants in PAPOLA

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

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

Position	Type	Phenotype	Significance	ClinVar
14-96502607-A-C			Benign (Mar 29, 2018)
14-96520119-C-G		not specified	Uncertain significance (Feb 28, 2023)
14-96520155-G-C		not specified	Likely benign (Aug 02, 2022)
14-96521023-A-G		not specified	Uncertain significance (Sep 27, 2024)
14-96521071-A-G		not specified	Uncertain significance (Oct 14, 2023)
14-96527475-G-A		not specified	Uncertain significance (Jul 09, 2024)
14-96531537-T-C			Benign (Dec 31, 2019)
14-96532402-A-G		not specified	Uncertain significance (Mar 10, 2025)
14-96532514-A-G		not specified	Uncertain significance (Dec 24, 2024)
14-96532550-G-A		not specified	Uncertain significance (Dec 31, 2024)
14-96532628-T-G		not specified	Uncertain significance (Jun 07, 2024)
14-96532645-A-C		not specified	Uncertain significance (Nov 10, 2024)
14-96535884-C-A		not specified	Uncertain significance (Dec 28, 2023)
14-96535912-A-G		not specified	Uncertain significance (Jan 17, 2025)
14-96542287-G-A		not specified	Uncertain significance (Jan 21, 2025)
14-96542776-T-A		not specified	Uncertain significance (Sep 20, 2024)
14-96542870-A-G		not specified	Likely benign (Oct 12, 2024)
14-96542875-C-T		not specified	Uncertain significance (Oct 27, 2022)
14-96544232-A-G		not specified	Uncertain significance (Mar 29, 2022)
14-96547861-A-G			Uncertain significance (-)
14-96552493-G-T		not specified	Uncertain significance (Nov 17, 2023)
14-96552499-A-G		not specified	Likely benign (Nov 19, 2022)
14-96552527-C-T			Benign (Mar 29, 2018)
14-96552537-A-G		not specified	Uncertain significance (Jul 14, 2023)
14-96552559-C-T		not specified	Uncertain significance (Nov 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAPOLA	protein_coding	protein_coding	ENST00000216277	22	65679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000196	125724	0	5	125729	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.55	190	386	0.492	0.0000188	4875
Missense in Polyphen		15	103.08	0.14552		1363
Synonymous	0.438	130	137	0.952	0.00000709	1436
Loss of Function	5.71	3	43.8	0.0686	0.00000220	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000882	0.0000882
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polymerase that creates the 3'-poly(A) tail of mRNA's. Also required for the endoribonucleolytic cleavage reaction at some polyadenylation sites. May acquire specificity through interaction with a cleavage and polyadenylation specificity factor (CPSF) at its C-terminus. {ECO:0000269|PubMed:19224921}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);polyadenylation of mrna;RNA Polymerase II Transcription;Metabolism of RNA;Processing of Intronless Pre-mRNAs;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Purine metabolism;mRNA Splicing - Major Pathway;TNFalpha;mRNA Splicing;mRNA 3,-end processing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.121
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.910
• hipred: Y
• hipred_score: 0.785
• ghis: 0.680

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Papola

Gene ontology

• Biological process: mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA polyadenylation;mRNA 3'-end processing;regulation of mRNA 3'-end processing;RNA polyadenylation
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: magnesium ion binding;RNA binding;polynucleotide adenylyltransferase activity;protein binding;ATP binding;manganese ion binding