HECTD2

HECT domain E3 ubiquitin protein ligase 2, the group of HECT domain containing

Basic information

Region (hg38): 10:91409279-91514829

Links

ENSG00000165338 ∙ NCBI:143279 ∙ ∙ HGNC:26736 ∙ Uniprot:Q5U5R9 ∙ 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 HECTD2 gene.

• Inborn genetic diseases (14 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HECTD2 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			12	2		14
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	2	2

Variants in HECTD2

This is a list of pathogenic ClinVar variants found in the HECTD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-91410457-G-C		not specified	Uncertain significance (Jan 17, 2023)
10-91410469-G-T		not specified	Uncertain significance (Jul 14, 2022)
10-91410526-G-C		not specified	Uncertain significance (Feb 21, 2024)
10-91410532-G-C		not specified	Uncertain significance (Mar 01, 2023)
10-91410550-G-C		not specified	Uncertain significance (May 31, 2023)
10-91410557-C-T		not specified	Uncertain significance (Oct 17, 2023)
10-91460471-C-T		not specified	Uncertain significance (May 17, 2023)
10-91460472-G-A		not specified	Uncertain significance (Jul 14, 2021)
10-91460474-A-G		not specified	Uncertain significance (Mar 29, 2023)
10-91460528-A-G		not specified	Likely benign (Feb 15, 2023)
10-91461300-C-A		not specified	Uncertain significance (Nov 10, 2022)
10-91461301-A-G		not specified	Uncertain significance (May 03, 2023)
10-91484598-C-T		not specified	Uncertain significance (Dec 08, 2023)
10-91485272-C-G		not specified	Uncertain significance (Aug 17, 2021)
10-91491275-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-91493495-G-A		not specified	Uncertain significance (Mar 07, 2024)
10-91496338-A-G		not specified	Likely benign (Oct 02, 2023)
10-91496340-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-91498138-T-C		not specified	Uncertain significance (Dec 27, 2023)
10-91498141-C-T		not specified	Likely benign (Apr 26, 2023)
10-91500570-G-A			Benign (Dec 31, 2019)
10-91500606-C-T			Benign (Dec 31, 2019)
10-91512373-G-A		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HECTD2	protein_coding	protein_coding	ENST00000298068	21	104491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00194	125684	0	7	125691	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.11	161	389	0.414	0.0000194	5059
Missense in Polyphen		13	101.59	0.12796		1332
Synonymous	1.95	110	139	0.790	0.00000719	1404
Loss of Function	5.36	6	44.7	0.134	0.00000233	572

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000685	0.0000685
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000366	0.0000352
Middle Eastern	0.0000557	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable 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|UniProtKB:Q69ZR2}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• loftool: 0.478
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.196
• hipred: Y
• hipred_score: 0.685
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.331

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hectd2
• Phenotype: reproductive system phenotype; skeleton phenotype

Gene ontology

• Biological process: protein polyubiquitination
• Cellular component: cytosol
• Molecular function: ubiquitin-protein transferase activity