PATL1

PAT1 homolog 1, processing body mRNA decay factor

Basic information

Region (hg38): 11:59636715-59669037

Links

ENSG00000166889 ∙ NCBI:219988 ∙ OMIM:614660 ∙ HGNC:26721 ∙ Uniprot:Q86TB9 ∙ 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 PATL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PATL1 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	4	5
missense			28	4		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	5	4

Variants in PATL1

This is a list of pathogenic ClinVar variants found in the PATL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59639081-C-T		not specified	Likely benign (Oct 14, 2023)
11-59639160-G-A		not specified	Uncertain significance (Jan 31, 2022)
11-59639325-T-G		not specified	Uncertain significance (Mar 15, 2024)
11-59639340-T-A		not specified	Uncertain significance (Apr 24, 2024)
11-59642978-T-A		not specified	Uncertain significance (Dec 19, 2023)
11-59647797-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-59647810-G-A		not specified	Uncertain significance (Jun 29, 2022)
11-59649516-T-C		not specified	Uncertain significance (Apr 26, 2023)
11-59649556-G-T		not specified	Uncertain significance (Jan 08, 2024)
11-59649566-A-G			Likely benign (Apr 04, 2018)
11-59649606-T-C		not specified	Uncertain significance (Nov 19, 2022)
11-59650764-A-G		not specified	Uncertain significance (Feb 01, 2023)
11-59650791-C-T		not specified	Uncertain significance (Aug 16, 2022)
11-59652470-T-C		not specified	Uncertain significance (Jan 30, 2024)
11-59652547-T-G		not specified	Uncertain significance (Oct 14, 2021)
11-59652556-G-A		not specified	Uncertain significance (May 26, 2022)
11-59652974-C-T		not specified	Uncertain significance (Feb 28, 2024)
11-59652975-G-A		not specified	Uncertain significance (Mar 13, 2023)
11-59654036-G-A			Benign (Jun 08, 2018)
11-59654059-T-C			Likely benign (Apr 04, 2018)
11-59655581-C-T		not specified	Uncertain significance (Dec 21, 2022)
11-59655644-G-T			Benign (Apr 16, 2018)
11-59655677-G-A			Likely benign (Jun 08, 2018)
11-59655712-T-G		not specified	Uncertain significance (Aug 08, 2023)
11-59655984-T-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PATL1	protein_coding	protein_coding	ENST00000300146	19	32265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.964	0.0360	124633	0	9	124642	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	278	418	0.665	0.0000226	4998
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000339	0.0000339
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000558	0.0000556
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000558	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: RNA degradation - Homo sapiens (human);Metabolism of RNA;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.666
• hipred: Y
• hipred_score: 0.825
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.333

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Patl1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• 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
• Cellular component: P-body;cytosol;PML body;nuclear speck;CCR4-NOT complex;cytoplasmic ribonucleoprotein granule
• Molecular function: RNA binding;protein binding;poly(U) RNA binding;poly(G) binding