PATL2

protein-coding

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

Gene summary

Predicted to enable RNA binding activity. Predicted to be involved in P-body assembly; deadenylation-dependent decapping of nuclear-transcribed mRNA; and negative regulation of translation. Predicted to act upstream of or within negative regulation of cytoplasmic mRNA processing body assembly. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001387263.1

Inheritance

ClinVar variants

P:22U:70B:21

Top phenotype

Oocyte/zygote/embryo maturation arrest 4

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr15:44,665,732-44,711,323

External References & Databases

Ensembl (ENSG00000229474)

Transcript & Mutation Effects

hg38 • Region Span ~45.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

oocyte maturation defect 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0021575

Submitter: PanelApp Australia

oocyte maturation defect 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0021575

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Oocyte/zygote/embryo maturation arrest 4AR

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

Comments: Attempts at IVF were not described as effective

Refs: 28965844; 28965849; 35091966

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PATL2 variants in ClinVar

6 Conditions Cataloged

Inborn genetic diseasesTotal: 66

Oocyte maturation defect 4Total: 30

not providedTotal: 13

PATL2-related disorderTotal: 10

not specifiedTotal: 2

Oocyte maturation defect 2Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001387263.1. 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	8 clinvar	1 clinvar	10
missense		6 clinvar	68 clinvar	10 clinvar	2 clinvar	86
nonsense	2 clinvar	4 clinvar	1 clinvar			7
start loss						0
frameshift	2 clinvar	3 clinvar				5
splice donor/acceptor (+/-2bp)	4 clinvar	1 clinvar				5
Total	8	14	70	18	3	113

Highest pathogenic variant AF is 0.00010310301

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001387263.1	RefSeq	NP_001374192.1	15	MANE Select
ENST00000682850.1	Ensembl	ENSP00000508024.1	15	MANE Select
NM_001145112.2	RefSeq	NP_001138584.1	15	Standard
NM_001330283.2	RefSeq	NP_001317212.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

RNA binding
protein binding

Cellular Component

P-body
nucleus
cytoplasm
ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000434130
Coding exons: 15
Length: 45585
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.48	209	279	0.750	0.0000147	3503
Missense (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

Population LoF Frequency

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

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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