HUWE1

HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1, the group of Armadillo like helical domain containing|MicroRNA protein coding host genes|HECT domain containing

Basic information

Region (hg38): X:53532095-53686752

Links

ENSG00000086758 ∙ NCBI:10075 ∙ OMIM:300697 ∙ HGNC:30892 ∙ Uniprot:Q7Z6Z7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, X-linked syndromic, Turner type (Definitive), mode of inheritance: XLD
• intellectual disability, X-linked syndromic, Turner type (Definitive), mode of inheritance: XL
• syndromic intellectual disability (Supportive), mode of inheritance: AD
• intellectual disability, X-linked syndromic, Turner type (Definitive), mode of inheritance: XL
• intellectual disability, X-linked syndromic, Turner type (Definitive), mode of inheritance: XL
• intellectual disability, X-linked syndromic, Turner type (Strong), mode of inheritance: XL
• non-syndromic X-linked intellectual disability (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked syndromic, Turner type; Xp11.22 microduplication syndrome	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic	25985138; 27130160; 27615324; 27884935; 29180823; 30797980
In Xp11.22 microduplication syndrome, the phenotype appears to be due to increased HUWE1 dosage

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HUWE1 gene.

• not provided (878 variants)
• Inborn genetic diseases (182 variants)
• Intellectual disability, X-linked syndromic, Turner type (141 variants)
• not specified (80 variants)
• HUWE1-related condition (17 variants)
• Intellectual disability (14 variants)
• Global developmental delay (2 variants)
• HUWE1-Related Disorder (2 variants)
• Trigonocephaly-short stature-developmental delay syndrome (2 variants)
• Non-syndromic X-linked intellectual disability (2 variants)
• X-linked intellectual disability (1 variants)
• Neurodevelopmental delay (1 variants)
• Autism spectrum disorder (1 variants)
• See cases (1 variants)
• Seizure;Intellectual disability (1 variants)
• HUWE1-related neurodevelopmental disorder (1 variants)
• 8 conditions (1 variants)
• Intellectual disability-hypotonic facies syndrome, X-linked, 1 (1 variants)
• Intellectual disability, X-linked 99 (1 variants)
• Abnormal corpus callosum morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HUWE1 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			7	139	50	196
missense	5	45	456	44	12	562
nonsense			2			2
start loss						0
frameshift	1		1			2
inframe indel		1	16	2	1	20
splice donor/acceptor (+/-2bp)	2	2	5	1		10
splice region			28	36	6	70
non coding		1	6	126	114	247
Total	8	49	493	312	177

Highest pathogenic variant AF is 0.00000920

Variants in HUWE1

This is a list of pathogenic ClinVar variants found in the HUWE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-53533364-C-T		HUWE1-related neurodevelopmental disorder • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 30, 2021)
X-53533365-G-A			Uncertain significance (Mar 01, 2021)
X-53533372-C-T			Likely benign (Dec 30, 2023)
X-53533418-AAAG-A			Likely benign (Aug 03, 2022)
X-53533447-A-G			Benign (Jul 15, 2021)
X-53533481-G-A			Likely benign (Dec 17, 2018)
X-53533990-C-G			Likely benign (Feb 22, 2023)
X-53533990-C-T			Likely benign (Dec 21, 2023)
X-53533995-C-T			Likely benign (Jun 23, 2022)
X-53534028-C-T			Uncertain significance (Jun 09, 2023)
X-53534033-T-G			Likely benign (Apr 25, 2018)
X-53534037-G-A			Uncertain significance (Sep 17, 2021)
X-53534039-C-G			Likely pathogenic (Jun 04, 2019)
X-53534049-C-T		Abnormal corpus callosum morphology	Conflicting classifications of pathogenicity (Sep 11, 2023)
X-53534071-T-A			Uncertain significance (Mar 09, 2018)
X-53534078-C-G			Uncertain significance (Jan 18, 2021)
X-53534081-G-A			Uncertain significance (Sep 04, 2019)
X-53534083-C-G			Likely pathogenic (Jan 10, 2023)
X-53534086-C-T			Uncertain significance (Mar 30, 2023)
X-53534100-C-T			Uncertain significance (Jan 08, 2021)
X-53534101-C-G		Intellectual disability, X-linked syndromic, Turner type	Pathogenic/Likely pathogenic (Jul 08, 2021)
X-53534125-C-T		Inborn genetic diseases	Likely pathogenic (Nov 30, 2016)
X-53534126-T-C			Benign (Feb 01, 2024)
X-53534126-T-G			Uncertain significance (Jun 29, 2023)
X-53534126-T-T		not specified • Inborn genetic diseases	Benign (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HUWE1	protein_coding	protein_coding	ENST00000342160	81	154617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.63e-22	125734	0	5	125739	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	8.87	697	1.74e+3	0.401	0.000139	28585
Missense in Polyphen		94	375.65	0.25023		6189
Synonymous	0.684	617	639	0.966	0.0000483	8866
Loss of Function	11.2	4	153	0.0261	0.0000125	2413

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000114	0.0000981
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000722	0.0000544
South Asian	0.000105	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which mediates ubiquitination and subsequent proteasomal degradation of target proteins. Regulates apoptosis by catalyzing the polyubiquitination and degradation of MCL1. Mediates monoubiquitination of DNA polymerase beta (POLB) at 'Lys-41', 'Lys-61' and 'Lys-81', thereby playing a role in base-excision repair. Also ubiquitinates the p53/TP53 tumor suppressor and core histones including H1, H2A, H2B, H3 and H4. Binds to an upstream initiator-like sequence in the preprodynorphin gene. Regulates neural differentiation and proliferation by catalyzing the polyubiquitination and degradation of MYCN. May regulate abundance of CDC6 after DNA damage by polyubiquitinating and targeting CDC6 to degradation. Mediates polyubiquitination of isoform 2 of PA2G4. {ECO:0000269|PubMed:15567145, ECO:0000269|PubMed:15767685, ECO:0000269|PubMed:15989956, ECO:0000269|PubMed:15989957, ECO:0000269|PubMed:17567951, ECO:0000269|PubMed:18488021, ECO:0000269|PubMed:19037095, ECO:0000269|PubMed:19713937}.
• Disease: DISEASE: Mental retardation, X-linked, syndromic, Turner type (MRXST) [MIM:300706]: A syndrome characterized by the association of mental retardation with macrocephaly and variable contractures. {ECO:0000269|PubMed:18252223}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, X-linked 17 (MRX17) [MIM:300705]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non- syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269|PubMed:18252223}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal microduplication involving HSD17B10 and HUWE1 has been found in patients with mental retardation.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;EGFR1;Validated targets of C-MYC transcriptional activation;p53 pathway (Consensus)

Recessive Scores

• pRec: 0.351

Intolerance Scores

• loftool: 0.136
• rvis_EVS: -3.36
• rvis_percentile_EVS: 0.4

Haploinsufficiency Scores

• pHI: 0.847
• hipred: Y
• hipred_score: 0.831
• ghis: 0.593

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.713

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Huwe1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; 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; 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); normal phenotype; embryo phenotype; immune system phenotype; renal/urinary system 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)

Gene ontology

• Biological process: protein polyubiquitination;base-excision repair;ubiquitin-dependent protein catabolic process;protein monoubiquitination;protein ubiquitination;histone ubiquitination;cell differentiation;neutrophil degranulation;positive regulation of protein targeting to mitochondrion
• Cellular component: extracellular region;nucleus;nucleoplasm;cytoplasm;cytosol;membrane;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: DNA binding;RNA binding;ubiquitin-protein transferase activity;protein binding;ubiquitin protein ligase activity