PABPC1L

protein-coding

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

Gene summary

This gene belongs to the polyadenylate-binding protein type-1 family of proteins. Members of this family bind to the polyA tails of mRNAs to regulate mRNA stability and translation. The mouse ortholog of this gene is required for female fertility. In human, expression of a functional protein is regulated by alternative splicing. The protein-coding splice variant for this gene is abundantly expressed in human oocytes, while a noncoding splice variant subject to nonsense-mediated decay is the predominant splice variant expressed in somatic tissues. [provided by RefSeq, Aug 2019]

Previous symbols:

C20orf119

MANE transcript

NM_001372179.1

Inheritance

ClinVar variants

P:10U:73B:9

Top phenotype

Oocyte/zygote/embryo maturation arrest 22

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr20:44,910,060-44,959,035

External References & Databases

Ensembl (ENSG00000101104)

Transcript & Mutation Effects

hg38 • Region Span ~49.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Oocyte/zygote/embryo maturation arrest 22AR

Manifestation: Obstetric

Intervention: General

Rationale: 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

Refs: 37052235; 37723834; 38177974

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PABPC1L variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 68

Oocyte/zygote/embryo maturation arrest 22Total: 8

not providedTotal: 5

Female infertility due to zona pellucida defectTotal: 1

Inherited oocyte maturation defectTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001372179.1. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	1 clinvar	3
missense	6 clinvar	1 clinvar	67 clinvar	7 clinvar		81
nonsense	2 clinvar		1 clinvar			3
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	9	1	73	8	1	92

Highest pathogenic variant AF is 0.00006527042

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001372179.1	RefSeq	NP_001359108.1	14	MANE Select
ENST00000217073.7	Ensembl	ENSP00000217073.3	14	MANE Select
ENST00000217074.9	Ensembl	ENSP00000217074.5	4	Standard
ENST00000217075.7	Ensembl	ENSP00000217075.3	5	Standard

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)

Biological Process

oocyte maturation
chromatin remodeling
mRNA polyadenylation
chromatin-mediated maintenance of transcription
nucleus localization

Molecular Function

RNA binding
mRNA 3'-UTR binding
poly(A) binding
poly(U) RNA binding

Cellular Component

nucleus
cytoplasm
cytosol
cytoplasmic stress granule
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000255136
Coding exons: 14
Length: 48974
Individuals with no LoFs: 124768
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 124793
p: 0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.37	314	390	0.805	0.0000245	3976
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.000065	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.138

Intolerance Scores

LoFtool: 0.344
RVIS EVS: 0.07
RVIS percentile EVS: 59.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.241

Gene Damage Prediction

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