HYAL3

hyaluronidase 3, the group of Hyaluronidases

Basic information

Region (hg38): 3:50292831-50299405

Links

ENSG00000186792 ∙ NCBI:8372 ∙ OMIM:604038 ∙ HGNC:5322 ∙ Uniprot:O43820 ∙ 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 HYAL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HYAL3 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						0
missense			30	4		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			21	2		23
Total	0	0	51	6	0

Variants in HYAL3

This is a list of pathogenic ClinVar variants found in the HYAL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50293263-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-50293321-G-C		not specified	Uncertain significance (Feb 27, 2023)
3-50293347-C-T		not specified	Uncertain significance (May 10, 2024)
3-50293353-G-T		not specified	Uncertain significance (Aug 14, 2024)
3-50293382-C-G		not specified	Uncertain significance (Dec 15, 2022)
3-50293391-C-T		not specified	Likely benign (Aug 04, 2024)
3-50293394-C-T		not specified	Uncertain significance (Aug 09, 2021)
3-50293421-C-T		not specified	Likely benign (Aug 26, 2024)
3-50293458-T-G		not specified	Uncertain significance (Jul 05, 2024)
3-50293640-T-A		not specified	Uncertain significance (May 09, 2023)
3-50293655-C-T		not specified	Uncertain significance (Apr 27, 2024)
3-50293670-C-T		not specified	Uncertain significance (Sep 15, 2021)
3-50294723-T-C		not specified	Uncertain significance (Feb 10, 2022)
3-50294726-C-T		not specified	Uncertain significance (Oct 09, 2024)
3-50294746-C-T		not specified	Uncertain significance (Dec 15, 2023)
3-50294801-A-G		not specified	Uncertain significance (Apr 29, 2024)
3-50294821-C-T		not specified	Uncertain significance (May 14, 2024)
3-50294894-C-T		not specified	Uncertain significance (Nov 09, 2021)
3-50294908-T-C		not specified	Uncertain significance (Dec 15, 2023)
3-50294909-G-A		not specified	Uncertain significance (Nov 12, 2021)
3-50294923-C-T		not specified	Uncertain significance (Oct 19, 2024)
3-50294924-G-A		not specified	Uncertain significance (Dec 02, 2022)
3-50294944-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-50294947-C-T		not specified	Likely benign (Dec 13, 2022)
3-50295043-A-C		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HYAL3	protein_coding	protein_coding	ENST00000336307	3	6638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.83e-7	0.591	125689	0	54	125743	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	205	254	0.806	0.0000155	2682
Missense in Polyphen		60	95.548	0.62796		1060
Synonymous	-1.10	114	100	1.14	0.00000544	898
Loss of Function	0.999	12	16.4	0.733	9.67e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000376	0.000376
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000220	0.000217
South Asian	0.000490	0.000490
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Facilitates sperm penetration into the layer of cumulus cells surrounding the egg by digesting hyaluronic acid. Involved in induction of the acrosome reaction in the sperm. Involved in follicular atresia, the breakdown of immature ovarian follicles that are not selected to ovulate. Induces ovarian granulosa cell apoptosis, possibly via apoptotic signaling pathway involving CASP8 and CASP3 activation, and poly(ADP-ribose) polymerase (PARP) cleavage. Has no hyaluronidase activity in embryonic fibroblasts in vitro. Has no hyaluronidase activity in granulosa cells in vitro. {ECO:0000250|UniProtKB:Q8VEI3}.
• Pathway: Glycosaminoglycan degradation - Homo sapiens (human);miR-targeted genes in muscle cell - TarBase;Metabolism of carbohydrates;CS/DS degradation;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism (Consensus)

Intolerance Scores

• loftool: 0.671
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.52

Haploinsufficiency Scores

• pHI: 0.0611
• hipred: N
• hipred_score: 0.239
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.214

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hyal3
• Phenotype: respiratory system phenotype; 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: ovarian follicle atresia;carbohydrate metabolic process;inflammatory response;penetration of zona pellucida;response to virus;hyaluronan catabolic process;response to antibiotic;viral entry into host cell;cartilage development;cellular response to interleukin-1;cellular response to tumor necrosis factor;cellular response to UV-B;negative regulation of ovarian follicle development;positive regulation of acrosomal vesicle exocytosis
• Cellular component: acrosomal vesicle;acrosomal membrane;extracellular region;lysosome;early endosome;endoplasmic reticulum;plasma membrane;cytoplasmic vesicle;sperm midpiece
• Molecular function: virus receptor activity;hyalurononglucosaminidase activity;protein binding;hyaluronoglucuronidase activity