PATL1

protein-coding

PAT1 homolog 1, processing body mRNA decay factor

Gene summary

Enables poly(G) binding activity and poly(U) RNA binding activity. Involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Located in CCR4-NOT complex and P-body. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152716.3

Inheritance

—

ClinVar variants

U:89B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr11:59,636,716-59,669,037

External References & Databases

Ensembl (ENSG00000166889)

Transcript & Mutation Effects

hg38 • Region Span ~32.3 kb

Loading mutation effect viewer...

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 PATL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152716.3. 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			3 clinvar	1 clinvar	4 clinvar	8
missense			82 clinvar	4 clinvar		86
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	89	5	4	98

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152716.3	RefSeq	NP_689929.2	19	MANE Select
ENST00000300146.10	Ensembl	ENSP00000300146.9	19	MANE Select
ENST00000894771.1	Ensembl	ENSP00000564830.1	18	Standard
ENST00000894771.2	Ensembl	ENSP00000564830.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA degradation - Homo sapiens (human)
Metabolism of RNA
mRNA decay by 5, to 3, exoribonuclease
Deadenylation-dependent mRNA decay

Biological Process

deadenylation-dependent decapping of nuclear-transcribed mRNA
cytoplasmic mRNA processing body assembly
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Molecular Function

RNA binding
protein binding
poly(U) RNA binding
poly(G) binding

Cellular Component

P-body
cytosol
PML body
nuclear speck
CCR4-NOT complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000300146
Coding exons: 19
Length: 32265
Individuals with no LoFs: 124633
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 124642
p: 0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.44	278	418	0.665	0.0000226	4998
Missense (PolyPhen)		61	133.31	0.45758		1742
Synonymous	0.336	138	143	0.964	0.00000680	1529
Loss of Function	5.16	8	45.6	0.175	0.00000292	468

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000034	0.000029	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. In case of infection, required for translation and replication of hepatitis C virus (HCV). {ECO:0000269|PubMed:17936923, ECO:0000269|PubMed:19628699, ECO:0000269|PubMed:20543818, ECO:0000269|PubMed:20584987, ECO:0000269|PubMed:20852261}.;

Recessive Scores

pRec: 0.0972

Intolerance Scores

RVIS EVS: 0.07
RVIS percentile EVS: 58.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.333

Gene Damage Prediction

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