HERC6

HECT and RLD domain containing E3 ubiquitin protein ligase family member 6, the group of HECT and RLD domain containing E3 ubiquitin protein ligases

Basic information

Region (hg38): 4:88378739-88443097

Links

ENSG00000138642 ∙ NCBI:55008 ∙ OMIM:609249 ∙ HGNC:26072 ∙ Uniprot:Q8IVU3 ∙ 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 HERC6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HERC6 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			77	7	4	88
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	77	7	7

Variants in HERC6

This is a list of pathogenic ClinVar variants found in the HERC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-88378938-G-C		not specified	Uncertain significance (Mar 21, 2024)
4-88378953-A-G		not specified	Likely benign (Feb 15, 2023)
4-88378960-G-T		not specified	Uncertain significance (Jun 02, 2023)
4-88378964-C-G		not specified	Uncertain significance (Mar 04, 2024)
4-88379024-T-G		not specified	Likely benign (Feb 23, 2025)
4-88379071-C-G		not specified	Uncertain significance (Jun 16, 2023)
4-88379073-G-A		not specified	Uncertain significance (Nov 25, 2024)
4-88383223-C-A		not specified	Uncertain significance (Jan 02, 2024)
4-88383226-A-G		not specified	Uncertain significance (Aug 20, 2024)
4-88383268-G-A		not specified	Uncertain significance (Apr 13, 2022)
4-88383278-A-C		not specified	Uncertain significance (Mar 10, 2025)
4-88383290-T-C		not specified	Uncertain significance (Jun 09, 2022)
4-88383319-G-C		not specified	Uncertain significance (Jun 13, 2023)
4-88385509-A-C		not specified	Uncertain significance (Dec 30, 2024)
4-88385516-A-G		not specified	Uncertain significance (Dec 31, 2024)
4-88385532-A-G		not specified	Uncertain significance (Dec 06, 2022)
4-88390660-G-A		not specified	Uncertain significance (Mar 08, 2024)
4-88390664-T-C		not specified	Uncertain significance (May 17, 2023)
4-88390682-G-A		not specified	Uncertain significance (Jan 31, 2025)
4-88390718-C-T		not specified	Uncertain significance (Aug 30, 2022)
4-88390730-C-T		not specified	Uncertain significance (Dec 03, 2021)
4-88390731-G-A			Benign (Jun 18, 2018)
4-88390772-T-C		not specified	Uncertain significance (Jan 23, 2024)
4-88390787-C-T		not specified	Uncertain significance (Dec 08, 2023)
4-88390805-C-G		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HERC6	protein_coding	protein_coding	ENST00000264346	23	64373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-14	0.918	125493	0	226	125719	0.000899

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	424	497	0.854	0.0000247	6656
Missense in Polyphen		140	162.52	0.86141		2320
Synonymous	1.30	160	182	0.878	0.00000951	1888
Loss of Function	2.16	29	44.6	0.651	0.00000207	629

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000625	0.000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000391	0.000381
Finnish	0.000234	0.000231
European (Non-Finnish)	0.000354	0.000343
Middle Eastern	0.000391	0.000381
South Asian	0.00525	0.00524
Other	0.000332	0.000326

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: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0805

Intolerance Scores

• loftool: 0.473
• rvis_EVS: 1.94
• rvis_percentile_EVS: 97.51

Haploinsufficiency Scores

• pHI: 0.0906
• hipred: N
• hipred_score: 0.132

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.337

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Herc6
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein polyubiquitination;hematopoietic progenitor cell differentiation;response to bacterium
• Cellular component: nucleus;cytosol
• Molecular function: ubiquitin-protein transferase activity