HAS1

hyaluronan synthase 1, the group of Glycosyltransferase family 2

Basic information

Region (hg38): 19:51713111-51723991

Previous symbols: [ "HAS" ]

Links

ENSG00000105509 ∙ NCBI:3036 ∙ OMIM:601463 ∙ HGNC:4818 ∙ Uniprot:Q92839 ∙ 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 HAS1 gene.

• Inborn genetic diseases (33 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAS1 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in HAS1

This is a list of pathogenic ClinVar variants found in the HAS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51713446-C-T		not specified	Uncertain significance (Dec 17, 2023)
19-51713477-C-T		not specified	Uncertain significance (Aug 08, 2023)
19-51713480-C-T		not specified	Uncertain significance (Oct 03, 2023)
19-51713491-A-G		not specified	Uncertain significance (Oct 05, 2023)
19-51713524-G-T		not specified	Uncertain significance (Nov 08, 2021)
19-51713527-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-51713558-C-T		not specified	Uncertain significance (Dec 17, 2021)
19-51713642-G-A		not specified	Uncertain significance (Aug 21, 2023)
19-51713648-G-C		not specified	Uncertain significance (Jul 14, 2022)
19-51713677-A-T		not specified	Uncertain significance (Jul 06, 2021)
19-51713710-T-C		not specified	Uncertain significance (Jun 29, 2022)
19-51713720-T-G		not specified	Uncertain significance (May 24, 2023)
19-51713752-C-T		not specified	Uncertain significance (Jul 08, 2022)
19-51713765-G-A		not specified	Uncertain significance (Oct 14, 2023)
19-51713792-T-G		not specified	Uncertain significance (Feb 17, 2024)
19-51713799-G-C		not specified	Uncertain significance (Sep 16, 2021)
19-51713807-G-A		not specified	Uncertain significance (Dec 09, 2023)
19-51713866-C-G		not specified	Uncertain significance (Jan 03, 2024)
19-51713921-C-T			Likely benign (Dec 31, 2019)
19-51716270-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-51716274-C-G		not specified	Uncertain significance (Nov 07, 2022)
19-51716283-C-A		not specified	Uncertain significance (Jun 26, 2023)
19-51716293-G-T		not specified	Uncertain significance (Jul 20, 2021)
19-51716345-C-A		not specified	Uncertain significance (Oct 20, 2021)
19-51716380-T-C		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAS1	protein_coding	protein_coding	ENST00000222115	5	10883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-12	0.0495	125702	1	45	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.475	374	349	1.07	0.0000224	3547
Missense in Polyphen		129	106.81	1.2078		1187
Synonymous	-0.783	177	164	1.08	0.0000111	1263
Loss of Function	0.249	19	20.2	0.940	9.59e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000873	0.000840
Ashkenazi Jewish	0.00	0.00
East Asian	0.000405	0.000381
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000405	0.000381
South Asian	0.000229	0.000196
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. Also able to catalyze the synthesis of chito- oligosaccharide depending on the substrate (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.245

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.287
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.617

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Has1
• Phenotype: normal phenotype

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;cell adhesion;negative regulation of fibroblast migration;hyaluronan biosynthetic process;cellular response to platelet-derived growth factor stimulus;estrous cycle;extracellular polysaccharide biosynthetic process;extracellular matrix assembly
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane
• Molecular function: protein binding;identical protein binding;hyaluronan synthase activity