HAS2
hyaluronan synthase 2, the group of Glycosyltransferase family 2
Basic information
Region (hg38): 8:121612116-121641440
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 12 | 12 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 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) | ||
| 8-121614260-G-A | not specified | Uncertain significance (Sep 04, 2024) | ||
| 8-121614354-C-T | not specified | Uncertain significance (Nov 28, 2024) | ||
| 8-121614485-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 8-121614529-G-C | Benign (Aug 08, 2018) | |||
| 8-121614572-T-A | not specified | Uncertain significance (Oct 21, 2024) | ||
| 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) | ||
| 8-121628838-G-A | not specified | Uncertain significance (Jun 19, 2024) | ||
| 8-121628920-C-T | not specified | Uncertain significance (Apr 08, 2023) | ||
| 8-121629095-G-T | not specified | Uncertain significance (Aug 08, 2023) | ||
| 8-121629183-A-G | not specified | Uncertain significance (Sep 02, 2024) | ||
| 8-121629189-G-C | not specified | Uncertain significance (May 02, 2024) | ||
| 8-121629303-A-G | not specified | Uncertain significance (Mar 18, 2024) |
GnomAD
Source:
| 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:
- 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