HAS2

hyaluronan synthase 2, the group of Glycosyltransferase family 2

Basic information

Region (hg38): 8:121612115-121641440

Links

ENSG00000170961 ∙ NCBI:3037 ∙ OMIM:601636 ∙ HGNC:4819 ∙ Uniprot:Q92819 ∙ 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 HAS2 gene.

• Inborn genetic diseases (9 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAS2 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	1
missense			9			9
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	10	0	1

Variants in HAS2

This is a list of pathogenic ClinVar variants found in the HAS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-121614163-A-T		not specified	Uncertain significance (Jun 11, 2021)
8-121614178-A-T			Uncertain significance (Oct 01, 2019)
8-121614198-C-A		not specified	Uncertain significance (Feb 06, 2024)
8-121614485-C-T		not specified	Uncertain significance (Aug 12, 2021)
8-121614529-G-C			Benign (Aug 08, 2018)
8-121614669-T-A		not specified	Uncertain significance (Jun 18, 2021)
8-121614742-T-C		not specified	Uncertain significance (Dec 21, 2023)
8-121614768-A-C		not specified	Uncertain significance (Aug 22, 2023)
8-121614770-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-121617167-C-T		not specified	Uncertain significance (Feb 06, 2023)
8-121628800-T-C		not specified	Uncertain significance (Jan 08, 2024)
8-121628830-C-T		not specified	Uncertain significance (Nov 22, 2021)
8-121628920-C-T		not specified	Uncertain significance (Apr 08, 2023)
8-121629095-G-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAS2	protein_coding	protein_coding	ENST00000303924	3	29275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00987	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.79	152	284	0.535	0.0000152	3627
Missense in Polyphen		29	127.2	0.22798		1676
Synonymous	-0.0628	107	106	1.01	0.00000613	1050
Loss of Function	4.03	2	22.7	0.0881	0.00000134	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the addition of GlcNAc or GlcUA monosaccharides to the nascent hyaluronan polymer. Therefore, it is essential to hyaluronan synthesis a major component of most extracellular matrices that has a structural role in tissues architectures and regulates cell adhesion, migration and differentiation. This is one of the isozymes catalyzing that reaction and it is particularly responsible for the synthesis of high molecular mass hyaluronan. Required for the transition of endocardial cushion cells into mesenchymal cells, a process crucial for heart development. May also play a role in vasculogenesis. High molecular mass hyaluronan also play a role in early contact inhibition a process which stops cell growth when cells come into contact with each other or the extracellular matrix (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.338

Intolerance Scores

• loftool: 0.0515
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.483
• hipred: Y
• hipred_score: 0.707
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Has2
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo 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; 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); growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: has2
• Affected structure: atrioventricular canal endocardium
• Phenotype tag: abnormal
• Phenotype quality: scaly

Gene ontology

• Biological process: vasculogenesis;kidney development;positive regulation of cell population proliferation;positive regulation of keratinocyte proliferation;positive regulation of smooth muscle cell migration;hyaluronan biosynthetic process;positive regulation of cell migration;positive regulation of urine volume;cellular response to platelet-derived growth factor stimulus;atrioventricular canal development;estrous cycle;extracellular polysaccharide biosynthetic process;positive regulation of keratinocyte migration;bone morphogenesis;renal water absorption;cellular response to interleukin-1;cellular response to tumor necrosis factor;cellular response to fluid shear stress;extracellular matrix assembly;endocardial cushion to mesenchymal transition;positive regulation of substrate adhesion-dependent cell spreading;positive regulation of hyaluronan biosynthetic process;positive regulation of monocyte aggregation;regulation of extracellular matrix assembly
• Cellular component: cytoplasm;integral component of plasma membrane
• Molecular function: protein binding;identical protein binding;hyaluronan synthase activity