PAPOLG

poly(A) polymerase gamma

Basic information

Region (hg38): 2:60756253-60802086

Links

ENSG00000115421 ∙ NCBI:64895 ∙ OMIM:616865 ∙ HGNC:14982 ∙ Uniprot:Q9BWT3 ∙ 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 PAPOLG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAPOLG 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1	1	2
splice region					1	1
non coding						0
Total	0	0	23	1	1

Variants in PAPOLG

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

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

Position	Type	Phenotype	Significance	ClinVar
2-60761755-G-A		not specified	Uncertain significance (Apr 14, 2022)
2-60768829-C-G		not specified	Uncertain significance (Mar 30, 2024)
2-60768883-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-60771544-C-G		not specified	Uncertain significance (Sep 23, 2023)
2-60771630-G-A			Uncertain significance (Jun 29, 2023)
2-60780778-G-A		not specified	Uncertain significance (Nov 30, 2022)
2-60781918-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-60782678-TAA-T			Benign (Nov 14, 2017)
2-60782680-A-ATTTTTTTTTTTTTT			Benign (Nov 14, 2017)
2-60782680-A-ATTTTTTTTTTTTTTTTTTTTTTT			Likely benign (Aug 18, 2017)
2-60782734-A-G		not specified	Uncertain significance (Jan 08, 2024)
2-60787057-A-G		not specified	Uncertain significance (Nov 23, 2021)
2-60787527-A-G		not specified	Uncertain significance (Oct 27, 2021)
2-60791823-G-A		not specified	Uncertain significance (Aug 19, 2023)
2-60791830-A-C		not specified	Uncertain significance (May 13, 2024)
2-60791879-A-T		not specified	Uncertain significance (Mar 15, 2024)
2-60792162-G-A		not specified	Uncertain significance (Feb 02, 2022)
2-60792247-C-T		not specified	Uncertain significance (Oct 16, 2023)
2-60792277-G-T		not specified	Uncertain significance (Nov 03, 2023)
2-60793628-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-60793973-G-A		not specified	Uncertain significance (Mar 19, 2024)
2-60793992-C-T		not specified	Uncertain significance (Mar 01, 2023)
2-60794000-C-T		not specified	Uncertain significance (Nov 14, 2023)
2-60794030-G-C		not specified	Uncertain significance (Dec 14, 2021)
2-60794054-A-G		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAPOLG	protein_coding	protein_coding	ENST00000238714	22	45856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00210	125726	0	18	125744	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	271	394	0.688	0.0000205	4793
Missense in Polyphen		28	101.07	0.27703		1302
Synonymous	0.993	120	135	0.891	0.00000685	1420
Loss of Function	5.35	6	44.5	0.135	0.00000239	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000895	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for the post-transcriptional adenylation of the 3'-terminal of mRNA precursors and several small RNAs including signal recognition particle (SRP) RNA, nuclear 7SK RNA, U2 small nuclear RNA, and ribosomal 5S RNA. {ECO:0000269|PubMed:11287430, ECO:0000269|PubMed:11463842}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);Purine metabolism (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.135
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.73

Haploinsufficiency Scores

• pHI: 0.432
• hipred: Y
• hipred_score: 0.527
• ghis: 0.652

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Papolg

Gene ontology

• Biological process: mRNA polyadenylation;RNA polyadenylation
• Cellular component: nucleus;nucleoplasm;cytosol;membrane;nuclear body
• Molecular function: RNA binding;polynucleotide adenylyltransferase activity;ATP binding;metal ion binding