PABPC1L

poly(A) binding protein cytoplasmic 1 like, the group of RNA binding motif containing

Basic information

Region (hg38): 20:44910060-44959035

Previous symbols: [ "C20orf119" ]

Links

ENSG00000101104 ∙ NCBI:80336 ∙ ∙ HGNC:15797 ∙ Uniprot:Q4VXU2 ∙ 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 PABPC1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABPC1L 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
missense			37	5		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	5	1

Variants in PABPC1L

This is a list of pathogenic ClinVar variants found in the PABPC1L region.

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

Position	Type	Phenotype	Significance	ClinVar
20-44910153-A-G		not specified	Uncertain significance (Aug 26, 2024)
20-44910207-G-A		not specified	Uncertain significance (Aug 05, 2024)
20-44910220-T-A		Inherited oocyte maturation defect	Likely pathogenic (Jan 27, 2020)
20-44910273-C-T		not specified	Uncertain significance (May 20, 2024)
20-44912666-G-A		not specified	Conflicting classifications of pathogenicity (Aug 01, 2022)
20-44912674-G-A		not specified	Uncertain significance (Sep 06, 2022)
20-44912691-G-C		not specified	Uncertain significance (May 24, 2023)
20-44912692-A-T		not specified	Uncertain significance (Mar 19, 2024)
20-44912716-A-C		not specified	Uncertain significance (Jun 09, 2022)
20-44912734-G-C		not specified	Uncertain significance (Nov 09, 2022)
20-44912747-G-A		not specified	Uncertain significance (Mar 31, 2024)
20-44912750-A-G		not specified	Uncertain significance (Sep 29, 2023)
20-44912773-A-G		not specified	Uncertain significance (Jun 05, 2023)
20-44916768-G-A		not specified	Uncertain significance (Jul 29, 2023)
20-44916768-G-C		not specified	Uncertain significance (Mar 18, 2024)
20-44916771-C-T		not specified	Uncertain significance (Mar 28, 2023)
20-44916784-G-C		not specified	Uncertain significance (Apr 08, 2022)
20-44916816-G-T		not specified	Uncertain significance (Nov 07, 2024)
20-44918908-T-C		not specified	Uncertain significance (Oct 29, 2021)
20-44918929-G-A		not specified	Uncertain significance (Sep 25, 2023)
20-44918936-G-C		not specified	Uncertain significance (Dec 15, 2022)
20-44918956-C-T			Likely benign (Aug 01, 2022)
20-44918957-G-A		not specified	Likely benign (Nov 26, 2024)
20-44919275-A-G		not specified	Uncertain significance (Feb 12, 2024)
20-44921604-A-G		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABPC1L	protein_coding	protein_coding	ENST00000255136	14	48974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000432	0.999	124768	0	25	124793	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	314	390	0.805	0.0000245	3976
Missense in Polyphen		105	153.88	0.68233		1610
Synonymous	-0.126	160	158	1.01	0.0000101	1225
Loss of Function	3.14	11	29.3	0.375	0.00000140	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000938	0.0000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000165
Finnish	0.00	0.00
European (Non-Finnish)	0.000162	0.000150
Middle Eastern	0.000167	0.000165
South Asian	0.0000654	0.0000653
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Pathway: RNA degradation - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.344
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.04

Haploinsufficiency Scores

• pHI: 0.151
• hipred: Y
• hipred_score: 0.591
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.241

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pabpc1l
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; hematopoietic system phenotype; reproductive system phenotype

Gene ontology

• Biological process: oocyte maturation;chromatin remodeling;mRNA polyadenylation;chromatin-mediated maintenance of transcription;nucleus localization
• Cellular component: nucleus;cytoplasm;cytosol;cytoplasmic stress granule;extracellular exosome;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;poly(A) binding;poly(U) RNA binding