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.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oocyte/zygote/embryo maturation arrest 22	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Obstetric	37052235; 37723834; 38177974

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PABPC1L gene.

not_specified (68 variants)
Oocyte/zygote/embryo_maturation_arrest_22 (8 variants)
not_provided (4 variants)
Female_infertility_due_to_zona_pellucida_defect (1 variants)
Inherited_oocyte_maturation_defect (1 variants)

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. These statistics are base on transcript: NM_001372179.1. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	1 clinvar	3
missense	6 clinvar	1 clinvar	67 clinvar	6 clinvar		80
nonsense	2 clinvar		1 clinvar			3
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	9	1	73	7	1

Highest pathogenic variant AF is 0.00006527042

Loading clinvar variants...

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
essential_gene_gene_trap
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