HECTD3

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

Basic information

Region (hg38): 1:45002540-45011324

Links

ENSG00000126107 ∙ NCBI:79654 ∙ OMIM:618638 ∙ HGNC:26117 ∙ Uniprot:Q5T447 ∙ 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 HECTD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HECTD3 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	2	3
missense			51	2	1	54
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	52	3	3

Variants in HECTD3

This is a list of pathogenic ClinVar variants found in the HECTD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-45003510-C-A		not specified	Uncertain significance (Apr 19, 2024)
1-45003568-A-G		not specified	Uncertain significance (Dec 17, 2023)
1-45003675-T-G		not specified	Uncertain significance (Apr 12, 2023)
1-45003724-C-T			Likely benign (Jul 02, 2018)
1-45003920-G-C		not specified	Uncertain significance (Aug 26, 2024)
1-45004105-A-C		not specified	Uncertain significance (Oct 01, 2024)
1-45004106-G-C		not specified	Uncertain significance (Jul 20, 2022)
1-45004118-G-C		not specified	Uncertain significance (Dec 03, 2021)
1-45004306-C-G		not specified	Uncertain significance (Jul 25, 2023)
1-45004328-A-T		not specified	Uncertain significance (Sep 30, 2024)
1-45004331-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-45004368-T-C		not specified	Uncertain significance (Aug 17, 2022)
1-45004611-T-C		not specified	Uncertain significance (Feb 08, 2025)
1-45004656-G-A		not specified	Uncertain significance (Nov 10, 2024)
1-45004664-T-C		not specified	Uncertain significance (Feb 10, 2023)
1-45004680-C-T		not specified	Uncertain significance (Nov 09, 2024)
1-45004766-G-A		not specified	Uncertain significance (Oct 20, 2023)
1-45004786-C-A		not specified	Uncertain significance (Oct 14, 2023)
1-45006007-T-G		not specified	Uncertain significance (Jun 12, 2023)
1-45006016-A-T		not specified	Uncertain significance (Nov 13, 2024)
1-45006038-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-45006064-C-T		not specified	Uncertain significance (Dec 14, 2021)
1-45006112-T-C			Benign (Jul 15, 2018)
1-45006708-A-G		not specified	Uncertain significance (May 18, 2023)
1-45006731-G-A			Benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HECTD3	protein_coding	protein_coding	ENST00000372172	21	8790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0888	0.911	124782	1	36	124819	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	367	503	0.730	0.0000312	5486
Missense in Polyphen		96	159.71	0.60109		1697
Synonymous	0.586	188	199	0.947	0.0000116	1745
Loss of Function	4.83	12	48.2	0.249	0.00000248	518

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000122
Ashkenazi Jewish	0.0000997	0.0000993
East Asian	0.000279	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000224	0.000221
Middle Eastern	0.000279	0.000278
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin ligases accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Mediates ubiquitination of TRIOBP and its subsequent proteasomal degradation, thus faciliting cell cycle progression by regulating the turn-over of TRIOBP. Mediates also ubiquitination of STX8 (By similarity). {ECO:0000250|UniProtKB:Q3U487, ECO:0000269|PubMed:18194665}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.637
• rvis_EVS: -0.91
• rvis_percentile_EVS: 10.07

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.563
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hectd3
• Phenotype: 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); digestive/alimentary phenotype; immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; normal 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process
• Cellular component: perinuclear region of cytoplasm
• Molecular function: ubiquitin-protein transferase activity;protein binding;syntaxin binding