PEG3

paternally expressed 3, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 19:56810077-56840728

Links

ENSG00000198300 ∙ NCBI:5178 ∙ OMIM:601483 ∙ HGNC:8826 ∙ Uniprot:Q9GZU2 ∙ 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 PEG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEG3 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				4	8	12
missense			110	22	10	142
nonsense				1		1
start loss						0
frameshift						0
inframe indel				2		2
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	110	29	18

Variants in PEG3

This is a list of pathogenic ClinVar variants found in the PEG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56813694-T-C		not specified	Uncertain significance (Oct 06, 2021)
19-56813704-C-T		not specified	Uncertain significance (Jan 02, 2024)
19-56813716-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-56813741-G-A			Benign (Dec 31, 2019)
19-56813766-G-C		not specified	Uncertain significance (May 23, 2023)
19-56813808-T-C		not specified	Uncertain significance (Aug 17, 2021)
19-56813818-A-G		not specified	Uncertain significance (Sep 14, 2023)
19-56813826-A-G		not specified	Uncertain significance (Jun 28, 2024)
19-56813922-C-G		not specified	Uncertain significance (Jan 23, 2024)
19-56813936-T-A			Benign/Likely benign (May 01, 2023)
19-56813949-A-G		not specified	Uncertain significance (Apr 22, 2024)
19-56813959-C-T		not specified	Uncertain significance (Oct 06, 2024)
19-56813982-A-G		not specified	Uncertain significance (Dec 01, 2022)
19-56813992-C-T		PEG3-related disorder	Likely benign (Dec 01, 2022)
19-56814001-C-T		not specified	Uncertain significance (Nov 25, 2024)
19-56814004-C-T		not specified	Uncertain significance (Apr 08, 2022)
19-56814016-C-G		not specified	Uncertain significance (Dec 20, 2023)
19-56814075-G-A			Benign (Nov 06, 2018)
19-56814141-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-56814144-A-G		not specified	Uncertain significance (Jul 20, 2022)
19-56814177-G-C			Likely benign (Dec 31, 2019)
19-56814187-TTGGCTCAGCAGCCTCCACTTC-T		PEG3-related disorder	Likely benign (Jul 20, 2020)
19-56814215-A-AGCAGCCTCCACTTCTGGCTCG			Likely benign (Dec 28, 2017)
19-56814275-G-A			Benign (Sep 19, 2018)
19-56814306-T-G		not specified	Uncertain significance (Sep 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEG3	protein_coding	protein_coding	ENST00000326441	7	30652

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000263	1.00	125537	0	211	125748	0.000839

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.954	957	877	1.09	0.0000498	10620
Missense in Polyphen		222	226.33	0.98086		2900
Synonymous	-0.194	324	320	1.01	0.0000186	2907
Loss of Function	4.43	18	52.7	0.341	0.00000298	685

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0183	0.00676
Ashkenazi Jewish	0.000331	0.000298
East Asian	0.00343	0.00332
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000196	0.000167
Middle Eastern	0.00343	0.00332
South Asian	0.000588	0.000588
Other	0.00148	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces apoptosis in cooperation with SIAH1A. Acts as a mediator between p53/TP53 and BAX in a neuronal death pathway that is activated by DNA damage. Acts synergistically with TRAF2 and inhibits TNF induced apoptosis through activation of NF-kappa-B (By similarity). Possesses a tumor suppressing activity in glioma cells. {ECO:0000250, ECO:0000269|PubMed:11260267}.
• Pathway: TNFalpha (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.696
• rvis_EVS: 1.51
• rvis_percentile_EVS: 95.45

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.319
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Peg3
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; reproductive system 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;apoptotic process;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;autophagosome
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding;metal ion binding