GeneBe

PABPC1

protein-coding

poly(A) binding protein cytoplasmic 1, the group of MicroRNA protein coding host genes|RNA binding motif containing

Gene summary

This gene encodes a poly(A) binding protein. The protein shuttles between the nucleus and cytoplasm and binds to the 3' poly(A) tail of eukaryotic messenger RNAs via RNA-recognition motifs. The binding of this protein to poly(A) promotes ribosome recruitment and translation initiation; it is also required for poly(A) shortening which is the first step in mRNA decay. The gene is part of a small gene family including three protein-coding genes and several pseudogenes.[provided by RefSeq, Aug 2010]

Previous symbols:
  • PAB1
  • PABPC2

MANE transcript

NM_002568.4

Inheritance

AD

ClinVar variants

P:2U:62B:9

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr8:100,685,816-100,722,809

External References & Databases

Ensembl (ENSG00000070756)NCBI Gene (26986)OMIM (604679)HGNC:8554GenCCUniProt (P11940)AlphaFoldClinVar (PABPC1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~37.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PABPC1 variants in ClinVar

9 Conditions Cataloged
not specifiedTotal: 22
not providedTotal: 6
EBV-positive nodal T- and NK-cell lymphomaTotal: 4
PABPC1-related conditionTotal: 3
Pulmonary artery atresiaTotal: 1
CIC-rearranged sarcomaTotal: 1
Neurodevelopmental disorderTotal: 1
TeratomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002568.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
4
clinvar
1
clinvar
 10
missense
1
clinvar
1
clinvar
34
clinvar
2
clinvar
 38
nonsense
1
clinvar
 1
start loss
0
frameshift
2
clinvar
2
clinvar
 4
splice donor/acceptor (+/-2bp)
20
clinvar
 20
Total11628173

Highest pathogenic variant AF is 0.0051461197

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 94 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002568.4RefSeqNP_002559.214MANE Select
ENST00000318607.10EnsemblENSP00000313007.514MANE Select
NM_001438282.1RefSeqNP_001425211.114Standard
ENST00000517403.5EnsemblENSP00000428190.15Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
pabpc1aDanio rerio

Structure: pigment cell

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • RNA degradation - Homo sapiens (human)
  • mRNA surveillance pathway - Homo sapiens (human)
  • RNA transport - Homo sapiens (human)
  • Translation Factors
  • Endoderm Differentiation

Biological Process

  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
  • mRNA splicing, via spliceosome
  • mRNA polyadenylation
  • translational initiation
  • gene silencing by RNA

Molecular Function

  • RNA binding
  • mRNA 3'-UTR binding
  • protein binding
  • protein C-terminus binding
  • poly(A) binding

Cellular Component

  • nucleus
  • cytoplasm
  • cytosol
  • focal adhesion
  • cytoplasmic stress granule

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000318607
Coding exons
14
Length
36994
Individuals with no LoFs
124412
Homozygous LoFs
0
Heterozygous LoFs
1333
Defined
125745
p
0.00531
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense4.491273700.3430.00002014130
Missense (PolyPhen)12102.290.117311255
Synonymous-0.2791181141.030.000005391210
Loss of Function4.76433.90.1180.00000190369

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00860.0075notable
Latino/Admixed American0.00610.0053notable
Ashkenazi Jewish0.00530.0045notable
East Asian0.00560.0049notable
Finnish0.00200.0018notable
European (Non-Finnish)0.00650.0055notable
South Asian0.00810.0068notable
Other0.00360.0031notable

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Binds the poly(A) tail of mRNA, including that of its own transcript. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA- binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding- region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. By binding to long poly(A) tails, may protect them from uridylation by ZCCHC6/ZCCHC11 and hence contribute to mRNA stability (PubMed:25480299). Positively regulates the replication of dengue virus (DENV) (PubMed:26735137). {ECO:0000269|PubMed:11051545, ECO:0000269|PubMed:17212783, ECO:0000269|PubMed:18447585, ECO:0000269|PubMed:20573744, ECO:0000269|PubMed:25480299, ECO:0000269|PubMed:26735137}.;

Recessive Scores

pRec
0.453

Intolerance Scores

RVIS EVS
-0.38
RVIS percentile EVS
27.42

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh
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