PABPC1

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

Basic information

Region (hg38): 8:100685816-100722809

Previous symbols: [ "PAB1", "PABPC2" ]

Links

ENSG00000070756 ∙ NCBI:26986 ∙ OMIM:604679 ∙ HGNC:8554 ∙ Uniprot:P11940 ∙ 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 PABPC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABPC1 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	1	2
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	5	1	2

Variants in PABPC1

This is a list of pathogenic ClinVar variants found in the PABPC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-100703359-T-TTTTAAACAGTTGGAACACCAGTGG		CIC-rearranged sarcoma	not provided (-)
8-100704305-G-A		not specified	Uncertain significance (Dec 21, 2022)
8-100704309-G-C		not specified	Uncertain significance (Jul 25, 2023)
8-100704316-G-A			Likely benign (Jan 01, 2023)
8-100705029-G-A		not specified	Uncertain significance (Jul 20, 2021)
8-100705064-C-T			Benign (Jul 31, 2018)
8-100705591-A-G		Pulmonary artery atresia	Pathogenic (-)
8-100706731-C-T		not specified	Uncertain significance (Jun 13, 2022)
8-100706758-C-T		not specified	Uncertain significance (Nov 30, 2021)
8-100709179-T-C			Benign (Jul 02, 2018)
8-100709528-A-C		PABPC1-related condition	Likely benign (Sep 16, 2024)
8-100709642-G-A		PABPC1-related condition	Likely benign (Sep 16, 2024)
8-100712361-C-T		not specified	Uncertain significance (Apr 24, 2024)
8-100712378-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
8-100712395-C-CA		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
8-100712397-CTT-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
8-100712798-C-CA			Benign (Aug 08, 2018)
8-100715538-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
8-100717892-G-A			Benign/Likely benign (Mar 01, 2022)
8-100718107-C-A		Teratoma	Uncertain significance (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABPC1	protein_coding	protein_coding	ENST00000318607	14	36994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00399	124412	0	1333	125745	0.00531

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.49	127	370	0.343	0.0000201	4130
Missense in Polyphen		12	102.29	0.11731		1255
Synonymous	-0.279	118	114	1.03	0.00000539	1210
Loss of Function	4.76	4	33.9	0.118	0.00000190	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0147	0.0135
Ashkenazi Jewish	0.00533	0.00447
East Asian	0.00560	0.00490
Finnish	0.00202	0.00185
European (Non-Finnish)	0.00645	0.00554
Middle Eastern	0.00560	0.00490
South Asian	0.00807	0.00682
Other	0.00358	0.00310

dbNSFP

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}.
• Pathway: RNA degradation - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Translation Factors;Endoderm Differentiation;regulation of eif-4e and p70s6 kinase;skeletal muscle hypertrophy is regulated via akt-mtor pathway;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;AUF1 (hnRNP D0) binds and destabilizes mRNA;Metabolism of RNA;Nonsense-Mediated Decay (NMD);Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);L13a-mediated translational silencing of Ceruloplasmin expression;Regulation of mRNA stability by proteins that bind AU-rich elements;Cap-dependent Translation Initiation;Deadenylation of mRNA;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.453

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.499
• hipred: Y
• hipred_score: 0.681
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pabpc1

Zebrafish Information Network

• Gene name: pabpc1a
• Affected structure: pigment cell
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mRNA splicing, via spliceosome;mRNA polyadenylation;translational initiation;gene silencing by RNA;regulation of mRNA stability;positive regulation of viral genome replication;positive regulation of translation;mRNA stabilization;positive regulation of nuclear-transcribed mRNA poly(A) tail shortening;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
• Cellular component: nucleus;cytoplasm;cytosol;focal adhesion;cytoplasmic stress granule;membrane;cytoplasmic ribonucleoprotein granule;extracellular exosome;catalytic step 2 spliceosome;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;protein C-terminus binding;poly(A) binding;poly(U) RNA binding;translation activator activity