PLAGL2

PLAG1 like zinc finger 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 20:32192504-32207743

Links

ENSG00000126003 ∙ NCBI:5326 ∙ OMIM:604866 ∙ HGNC:9047 ∙ Uniprot:Q9UPG8 ∙ 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 PLAGL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLAGL2 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						0
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in PLAGL2

This is a list of pathogenic ClinVar variants found in the PLAGL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-32196475-G-A		not specified	Uncertain significance (May 26, 2022)
20-32196484-T-C		not specified	Uncertain significance (Sep 30, 2024)
20-32196571-G-T		not specified	Uncertain significance (Mar 16, 2024)
20-32196591-G-C		not specified	Uncertain significance (Oct 26, 2022)
20-32196603-T-C		not specified	Uncertain significance (Oct 08, 2024)
20-32196646-C-T		not specified	Uncertain significance (Aug 12, 2021)
20-32196672-T-C		not specified	Uncertain significance (Jun 23, 2021)
20-32196701-G-C		not specified	Uncertain significance (Apr 11, 2023)
20-32196763-C-T		not specified	Uncertain significance (Aug 17, 2022)
20-32196765-T-C		not specified	Uncertain significance (Aug 10, 2023)
20-32196789-G-A		not specified	Uncertain significance (Aug 23, 2021)
20-32196792-G-A		not specified	Uncertain significance (Aug 05, 2024)
20-32196835-G-T		not specified	Uncertain significance (Mar 19, 2024)
20-32196843-G-C		not specified	Uncertain significance (Mar 14, 2023)
20-32196922-T-G		not specified	Uncertain significance (Oct 14, 2021)
20-32196964-G-C		not specified	Uncertain significance (Mar 30, 2024)
20-32196967-G-A		not specified	Uncertain significance (Nov 28, 2023)
20-32197011-G-C		not specified	Uncertain significance (Nov 09, 2023)
20-32197015-C-T		not specified	Likely benign (Jul 09, 2021)
20-32197020-G-A		not specified	Uncertain significance (Aug 20, 2024)
20-32197083-T-C		not specified	Uncertain significance (Jun 29, 2023)
20-32197093-T-C		not specified	Uncertain significance (Feb 19, 2025)
20-32197102-G-A		not specified	Uncertain significance (Mar 06, 2025)
20-32197124-G-T		not specified	Uncertain significance (Aug 20, 2023)
20-32197155-C-T		not specified	Uncertain significance (Jan 17, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLAGL2	protein_coding	protein_coding	ENST00000246229	2	15289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0175	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	198	301	0.658	0.0000182	3217
Missense in Polyphen		63	116.87	0.53908		1318
Synonymous	-0.284	131	127	1.03	0.00000780	1045
Loss of Function	3.25	0	12.3	0.00	5.22e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000626	0.0000615
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Shows weak transcriptional activatory activity.

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.233
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.873
• hipred: Y
• hipred_score: 0.728
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plagl2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; 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); digestive/alimentary phenotype

Gene ontology

• Biological process: lipid metabolic process;post-embryonic development;chylomicron assembly;positive regulation of transcription by RNA polymerase II;positive regulation of intrinsic apoptotic signaling pathway
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding;metal ion binding