HERC3

HECT and RLD domain containing E3 ubiquitin protein ligase 3, the group of HECT and RLD domain containing E3 ubiquitin protein ligases

Basic information

Region (hg38): 4:88592433-88708541

Links

ENSG00000138641 ∙ NCBI:8916 ∙ OMIM:605200 ∙ HGNC:4876 ∙ Uniprot:Q15034 ∙ 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 HERC3 gene.

• Inborn genetic diseases (32 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HERC3 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				2		2
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			14	1		15
Total	0	0	31	4	0

Variants in HERC3

This is a list of pathogenic ClinVar variants found in the HERC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-88605914-A-G		not specified	Uncertain significance (Jul 15, 2021)
4-88649863-C-G		not specified	Uncertain significance (Jan 26, 2023)
4-88649992-G-A		not specified	Uncertain significance (Jun 28, 2023)
4-88652084-G-A			Likely benign (Mar 01, 2023)
4-88652960-G-A			Likely benign (Nov 01, 2023)
4-88653087-A-G		not specified	Likely benign (Feb 22, 2023)
4-88655225-G-A		not specified	Uncertain significance (Aug 08, 2023)
4-88655232-T-C		not specified	Uncertain significance (May 10, 2022)
4-88658461-C-A		not specified	Uncertain significance (May 24, 2023)
4-88662435-A-G		not specified	Uncertain significance (Jan 09, 2024)
4-88664211-A-G		not specified	Uncertain significance (Nov 22, 2023)
4-88667397-C-T		not specified	Uncertain significance (Dec 11, 2023)
4-88667940-C-T		not specified	Uncertain significance (Jan 29, 2024)
4-88669900-G-T		not specified	Uncertain significance (May 31, 2023)
4-88669910-C-G		not specified	Uncertain significance (Dec 21, 2022)
4-88670013-A-G		not specified	Uncertain significance (Feb 23, 2023)
4-88678012-C-G		not specified	Uncertain significance (Oct 20, 2023)
4-88678013-T-G		not specified	Uncertain significance (Apr 07, 2023)
4-88678028-C-T		not specified	Uncertain significance (Nov 10, 2022)
4-88680124-C-T		not specified	Uncertain significance (Dec 13, 2022)
4-88680126-G-A		not specified	Uncertain significance (Jan 30, 2024)
4-88680141-G-A		not specified	Uncertain significance (Apr 11, 2023)
4-88680166-A-T		not specified	Uncertain significance (Oct 25, 2022)
4-88680199-A-G		not specified	Uncertain significance (Oct 22, 2021)
4-88681195-A-G		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HERC3	protein_coding	protein_coding	ENST00000402738	24	187495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0701	0.930	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.21	338	550	0.614	0.0000266	6906
Missense in Polyphen		105	244.82	0.42889		3053
Synonymous	0.579	197	208	0.949	0.0000105	1995
Loss of Function	5.23	14	56.4	0.248	0.00000264	694

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000330	0.000326
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000330	0.000326
South Asian	0.000132	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. {ECO:0000250}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.478
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.11

Haploinsufficiency Scores

• pHI: 0.238
• hipred: Y
• hipred_score: 0.694
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Herc3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: cytosol;cytoplasmic vesicle
• Molecular function: ubiquitin-protein transferase activity