PAN3

poly(A) specific ribonuclease subunit PAN3

Basic information

Region (hg38): 13:28138506-28295335

Links

ENSG00000152520 ∙ NCBI:255967 ∙ OMIM:617448 ∙ HGNC:29991 ∙ Uniprot:Q58A45 ∙ 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 PAN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAN3 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			52			52
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	0	0

Variants in PAN3

This is a list of pathogenic ClinVar variants found in the PAN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-28138680-C-T		not specified	Uncertain significance (Nov 07, 2024)
13-28138698-C-T		not specified	Uncertain significance (Jan 26, 2023)
13-28138707-C-A		not specified	Uncertain significance (Dec 20, 2023)
13-28138727-G-A		not specified	Uncertain significance (Sep 29, 2023)
13-28138740-T-G		not specified	Uncertain significance (Jul 30, 2024)
13-28138740-TG-T		not specified	Uncertain significance (Aug 19, 2021)
13-28138755-T-G		not specified	Uncertain significance (Sep 16, 2021)
13-28138778-G-T		not specified	Uncertain significance (Jan 08, 2025)
13-28138779-C-T		not specified	Uncertain significance (Jan 08, 2025)
13-28138781-G-T		not specified	Uncertain significance (Dec 18, 2023)
13-28138784-G-A		not specified	Uncertain significance (Feb 05, 2024)
13-28138886-C-T		not specified	Uncertain significance (Jul 07, 2024)
13-28138919-C-G		not specified	Uncertain significance (Feb 08, 2025)
13-28138935-C-G		not specified	Uncertain significance (Sep 14, 2022)
13-28138961-G-C		not specified	Uncertain significance (Jan 01, 2025)
13-28138965-T-G		not specified	Uncertain significance (Jun 11, 2021)
13-28138988-C-T		not specified	Uncertain significance (Nov 25, 2024)
13-28139016-G-C		not specified	Uncertain significance (Jul 23, 2024)
13-28139042-G-A		not specified	Uncertain significance (Mar 27, 2023)
13-28174304-A-G		not specified	Uncertain significance (Feb 28, 2024)
13-28174323-A-C		not specified	Uncertain significance (Jul 09, 2024)
13-28174331-A-G		not specified	Uncertain significance (Jun 18, 2021)
13-28174362-G-A		not specified	Uncertain significance (Apr 29, 2022)
13-28176515-C-T		not specified	Uncertain significance (Jun 28, 2023)
13-28176556-C-T		not specified	Uncertain significance (Nov 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAN3	protein_coding	protein_coding	ENST00000380958	19	156833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000741	125507	0	3	125510	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	285	432	0.659	0.0000214	5734
Missense in Polyphen		73	171.13	0.42657		2176
Synonymous	0.310	145	150	0.968	0.00000740	1783
Loss of Function	5.72	2	42.0	0.0477	0.00000243	507

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)	0.0000268	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in general and miRNA-mediated mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein (PABP). PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by XRN1. PAN3 acts as a positive regulator for PAN activity, recruiting the catalytic subunit PAN2 to mRNA via its interaction with RNA and PABP, and to miRNA targets via its interaction with GW182 family proteins. {ECO:0000255|HAMAP-Rule:MF_03181, ECO:0000269|PubMed:14583602, ECO:0000269|PubMed:23932717}.
• Pathway: RNA degradation - Homo sapiens (human);Metabolism of RNA;Deadenylation of mRNA;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.608
• hipred: Y
• hipred_score: 0.728
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.831

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pan3

Gene ontology

• Biological process: nuclear-transcribed mRNA poly(A) tail shortening;deadenylation-dependent decapping of nuclear-transcribed mRNA;mRNA processing;protein phosphorylation;protein targeting;positive regulation of cytoplasmic mRNA processing body assembly;RNA phosphodiester bond hydrolysis, exonucleolytic
• Cellular component: P-body;cytosol;PAN complex
• Molecular function: RNA binding;poly(A)-specific ribonuclease activity;protein kinase activity;protein binding;ATP binding;metal ion binding