PAN3

poly(A) specific ribonuclease subunit PAN3

Basic information

Region (hg38): 13:28138506-28295335

Links

ENSG00000152520NCBI:255967OMIM:617448HGNC:29991Uniprot:Q58A45AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PAN3 gene.

  • not_specified (78 variants)

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. These statistics are base on transcript: NM_000175854.8. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
76
clinvar
1
clinvar
77
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 0 0 77 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PAN3protein_codingprotein_codingENST00000380958 19156833
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000741125507031255100.0000120
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.522854320.6590.00002145734
Missense in Polyphen73171.130.426572176
Synonymous0.3101451500.9680.000007401783
Loss of Function5.72242.00.04770.00000243507

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002680.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pan3
Phenotype

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