PATL2

PAT1 homolog 2, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 15:44665731-44711323

Links

ENSG00000229474 ∙ NCBI:197135 ∙ OMIM:614661 ∙ HGNC:33630 ∙ Uniprot:C9JE40 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oocyte maturation defect 4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oocyte/zygote/embryo maturation arrest 4	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	28965844; 28965849; 35091966
Attempts at IVF were not described as effective

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PATL2 gene.

• Inborn genetic diseases (17 variants)
• Oocyte maturation defect 4 (11 variants)
• not provided (6 variants)
• Oocyte maturation defect 2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PATL2 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	1	2
missense		2	19	3	1	25
nonsense	1	2				3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1	1				2
splice region			1			1
non coding			1			1
Total	2	5	20	4	2

Highest pathogenic variant AF is 0.0000263

Variants in PATL2

This is a list of pathogenic ClinVar variants found in the PATL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-44665812-A-T			Uncertain significance (Aug 01, 2021)
15-44666410-T-G		Inborn genetic diseases	Uncertain significance (May 27, 2022)
15-44666454-T-C			Benign (Jul 06, 2018)
15-44666475-G-C			Likely benign (Jul 05, 2018)
15-44667116-G-A			Uncertain significance (Feb 01, 2024)
15-44667151-G-A		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
15-44667155-C-T		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
15-44667158-G-T		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
15-44667176-G-T		Inborn genetic diseases	Uncertain significance (May 04, 2023)
15-44668359-C-T		PATL2-related disorder	Likely benign (Nov 09, 2023)
15-44668367-G-A		Inborn genetic diseases	Uncertain significance (Jul 30, 2023)
15-44668397-G-A		Inborn genetic diseases	Likely benign (Mar 29, 2023)
15-44668431-G-A		Inborn genetic diseases	Likely benign (Jan 04, 2022)
15-44668433-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
15-44668467-A-G		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
15-44668484-T-C		Oocyte maturation defect 4	Pathogenic (Jan 31, 2020)
15-44668485-G-T			Uncertain significance (Apr 15, 2021)
15-44668978-A-G		Oocyte maturation defect 4	Pathogenic (Apr 10, 2023)
15-44668982-G-C			Uncertain significance (Feb 01, 2023)
15-44668999-C-T			Uncertain significance (Dec 01, 2023)
15-44669030-C-T		Inborn genetic diseases	Uncertain significance (Nov 03, 2023)
15-44669058-G-C		PATL2-related disorder	Likely benign (Jul 16, 2019)
15-44669096-C-T		Oocyte maturation defect 4	Uncertain significance (Apr 16, 2018)
15-44669105-C-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
15-44669326-C-T		Inborn genetic diseases	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PATL2	protein_coding	protein_coding	ENST00000434130	15	45585

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-11	0.754	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	209	279	0.750	0.0000147	3503
Missense in Polyphen		54	82.868	0.65164		1163
Synonymous	1.23	95	111	0.852	0.00000596	1076
Loss of Function	1.65	22	32.1	0.685	0.00000164	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that acts as a translational repressor. {ECO:0000250|UniProtKB:Q4V7K4}.

Intolerance Scores

• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Patl2
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: deadenylation-dependent decapping of nuclear-transcribed mRNA;negative regulation of cytoplasmic mRNA processing body assembly;negative regulation of translation;cytoplasmic mRNA processing body assembly
• Cellular component: P-body;nucleus;cytoplasm;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding