PELI2

pellino E3 ubiquitin protein ligase family member 2, the group of Pellino E3 ubiquitin protein ligases

Basic information

Region (hg38): 14:56117813-56301524

Links

ENSG00000139946 ∙ NCBI:57161 ∙ OMIM:614798 ∙ HGNC:8828 ∙ Uniprot:Q9HAT8 ∙ 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 PELI2 gene.

• Inborn genetic diseases (12 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PELI2 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
missense			12		1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	2

Variants in PELI2

This is a list of pathogenic ClinVar variants found in the PELI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-56118714-A-T		not specified	Uncertain significance (Aug 13, 2021)
14-56178379-G-A		not specified	Uncertain significance (Jan 04, 2022)
14-56178409-C-G		not specified	Uncertain significance (Jul 26, 2022)
14-56178448-C-T		not specified	Uncertain significance (Nov 03, 2023)
14-56279705-A-G		not specified	Uncertain significance (Dec 13, 2023)
14-56288518-A-G		not specified	Uncertain significance (Jun 28, 2022)
14-56288588-G-A		not specified	Uncertain significance (Nov 07, 2023)
14-56288590-A-G		not specified	Uncertain significance (Feb 23, 2023)
14-56290297-C-G		not specified	Uncertain significance (Dec 02, 2022)
14-56290328-G-A		not specified	Uncertain significance (Aug 02, 2022)
14-56290386-G-A			Benign (Dec 18, 2018)
14-56290426-A-C		not specified	Uncertain significance (Dec 19, 2023)
14-56296737-C-T			Benign (Sep 12, 2018)
14-56296793-A-G		not specified	Uncertain significance (Dec 21, 2022)
14-56296794-C-G		not specified	Uncertain significance (Sep 22, 2023)
14-56296886-C-T		not specified	Uncertain significance (Feb 16, 2023)
14-56296930-C-G		not specified	Uncertain significance (Oct 27, 2022)
14-56297075-A-G		not specified	Uncertain significance (Feb 22, 2023)
14-56297086-G-A		not specified	Uncertain significance (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PELI2	protein_coding	protein_coding	ENST00000267460	6	183713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.830	0.170	125731	0	7	125738	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	186	258	0.720	0.0000154	2747
Missense in Polyphen		67	118.44	0.56567		1212
Synonymous	-1.21	122	106	1.15	0.00000758	819
Loss of Function	3.40	3	19.0	0.158	0.00000108	203

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	0.0000462	0.0000462
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. Involved in the TLR and IL-1 signaling pathways via interaction with the complex containing IRAK kinases and TRAF6. Mediates IL1B-induced IRAK1 'Lys-63'-linked polyubiquitination and possibly 'Lys-48'-linked ubiquitination. May be important for LPS- and IL1B-induced MAP3K7- dependent, but not MAP3K3-dependent, NF-kappa-B activation. Can activate the MAP (mitogen activated protein) kinase pathway leading to activation of ELK1. {ECO:0000269|PubMed:12804775, ECO:0000269|PubMed:12860405, ECO:0000269|PubMed:17675297, ECO:0000269|PubMed:17997719, ECO:0000269|PubMed:22669975}.
• Pathway: Regulation of toll-like receptor signaling pathway;IL-1 signaling pathway;Toll Like Receptor 7/8 (TLR7/8) Cascade;Signaling by Interleukins;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Interleukin-1 signaling;IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation;Innate Immune System;Immune System;IL1;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;Toll Like Receptor 4 (TLR4) Cascade;IRAK1 recruits IKK complex;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.0525
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.775
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.673

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Peli2

Gene ontology

• Biological process: protein polyubiquitination;positive regulation of protein phosphorylation;protein phosphorylation;Toll signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of MAPK cascade;interleukin-1-mediated signaling pathway
• Cellular component: cytosol
• Molecular function: protein serine/threonine kinase activity;protein binding;ubiquitin-ubiquitin ligase activity;ubiquitin protein ligase activity