HSP90B1

heat shock protein 90 beta family member 1, the group of MicroRNA protein coding host genes|Heat shock 90kDa proteins

Basic information

Region (hg38): 12:103930106-103953931

Previous symbols: [ "TRA1" ]

Links

ENSG00000166598 ∙ NCBI:7184 ∙ OMIM:191175 ∙ HGNC:12028 ∙ Uniprot:P14625 ∙ 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 HSP90B1 gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSP90B1 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	2
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in HSP90B1

This is a list of pathogenic ClinVar variants found in the HSP90B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-103930531-G-T		not specified	Uncertain significance (Aug 17, 2021)
12-103931545-T-C		not specified	Uncertain significance (Feb 28, 2023)
12-103932301-T-G		not specified	Uncertain significance (Jun 29, 2023)
12-103932324-G-A		not specified	Uncertain significance (Feb 28, 2023)
12-103932342-C-G		not specified	Uncertain significance (Dec 19, 2023)
12-103932343-G-A			Benign (Apr 25, 2018)
12-103932901-A-G		not specified	Uncertain significance (Dec 07, 2021)
12-103934055-A-G		not specified	Uncertain significance (Aug 28, 2023)
12-103934187-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-103934227-A-G		not specified	Uncertain significance (Oct 29, 2021)
12-103937718-C-T		not specified	Uncertain significance (Feb 08, 2023)
12-103937753-G-A		not specified	Uncertain significance (Apr 25, 2022)
12-103937783-C-A		not specified	Uncertain significance (Oct 27, 2023)
12-103938421-G-A		not specified	Uncertain significance (Dec 05, 2022)
12-103939557-A-G		not specified	Uncertain significance (Sep 20, 2023)
12-103941512-G-A		not specified	Uncertain significance (Apr 11, 2023)
12-103942549-G-A		not specified	Uncertain significance (Oct 20, 2021)
12-103942596-G-T		not specified	Uncertain significance (Oct 12, 2022)
12-103942665-C-T		not specified	Uncertain significance (Nov 22, 2023)
12-103943275-G-C		not specified	Uncertain significance (Jul 20, 2022)
12-103943308-C-T		not specified	Uncertain significance (Jul 06, 2021)
12-103946689-G-A		not specified	Uncertain significance (Sep 15, 2021)
12-103946818-T-G			Likely benign (Oct 01, 2021)
12-103946825-G-A		not specified	Uncertain significance (Oct 12, 2022)
12-103946850-G-A		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSP90B1	protein_coding	protein_coding	ENST00000299767	18	23539

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00280	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	307	431	0.712	0.0000226	5333
Missense in Polyphen		88	173.48	0.50725		2132
Synonymous	0.195	152	155	0.980	0.00000873	1437
Loss of Function	5.29	6	43.7	0.137	0.00000226	553

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000235	0.000217
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.0000645	0.0000615
Middle Eastern	0.000235	0.000217
South Asian	0.0000997	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Molecular chaperone that functions in the processing and transport of secreted proteins. When associated with CNPY3, required for proper folding of Toll-like receptors (By similarity). Functions in endoplasmic reticulum associated degradation (ERAD). Has ATPase activity. {ECO:0000250, ECO:0000269|PubMed:18264092}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);ATF6 (ATF6-alpha) activates chaperone genes;Photodynamic therapy-induced unfolded protein response;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Prion disease pathway;Interleukin-4 and 13 signaling;PI3K-Akt Signaling Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Vesicle-mediated transport;Post-translational protein phosphorylation;Trafficking and processing of endosomal TLR;Toll-Like Receptors Cascades;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;AndrogenReceptor;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors;IL6-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.429

Intolerance Scores

• loftool: 0.297
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.858
• hipred: Y
• hipred_score: 0.736
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsp90b1
• Phenotype: immune system phenotype; pigmentation 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); 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; embryo phenotype; cellular 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); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: hsp90b1
• Affected structure: muscle cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: response to hypoxia;toll-like receptor signaling pathway;receptor-mediated endocytosis;protein transport;cytokine-mediated signaling pathway;ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;actin rod assembly;protein folding in endoplasmic reticulum;response to endoplasmic reticulum stress;ATF6-mediated unfolded protein response;negative regulation of apoptotic process;regulation of phosphoprotein phosphatase activity;post-translational protein modification;cellular protein metabolic process;sequestering of calcium ion;cellular response to ATP
• Cellular component: extracellular region;nucleus;endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;cytosol;plasma membrane;focal adhesion;membrane;midbody;protein-containing complex;endoplasmic reticulum chaperone complex;melanosome;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome;endocytic vesicle lumen
• Molecular function: RNA binding;calcium ion binding;protein binding;ATP binding;protein phosphatase binding;low-density lipoprotein particle receptor binding;unfolded protein binding