PABPN1L

protein-coding

PABPN1 like, cytoplasmic, the group of RNA binding motif containing

Gene summary

Predicted to enable poly(A) binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay. Predicted to act upstream of or within maternal-to-zygotic transition of gene expression; negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process; and negative regulation of protein ubiquitination. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001080487.4

Inheritance

—

ClinVar variants

U:70B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.39

Max pathogenic AF

—

Genomic locus

chr16:88,863,333-88,866,660

External References & Databases

Ensembl (ENSG00000205022)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PABPN1L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 77

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080487.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			70 clinvar	7 clinvar		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	7	0	77

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080487.4	RefSeq	NP_001073956.2	7	MANE Select
ENST00000419291.7	Ensembl	ENSP00000408598.2	7	MANE Select
NM_001294328.4	RefSeq	NP_001281257.1	6	Standard
NM_001385709.2	RefSeq	NP_001372638.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Influenza A - Homo sapiens (human)
mRNA surveillance pathway - Homo sapiens (human)

Molecular Function

RNA binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000419291
Coding exons: 7
Length: 5035
Individuals with no LoFs: 123902
Homozygous LoFs: 0
Heterozygous LoFs: 80
Defined: 123982
p: 0.000323

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.838	191	161	1.19	0.00000971	1741
Missense (PolyPhen)		34	34.008	0.99977		382
Synonymous	-1.20	84	71.1	1.18	0.00000489	541
Loss of Function	-1.42	21	15.1	1.39	8.86e-7	155

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00064	0.00059	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0017	0.0017	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00022	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds the poly(A) tail of mRNA. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.686
RVIS EVS: 1.62
RVIS percentile EVS: 96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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