HSBP1

heat shock factor binding protein 1

Basic information

Region (hg38): 16:83719310-83819737

Links

ENSG00000230989 ∙ NCBI:3281 ∙ OMIM:604553 ∙ HGNC:5203 ∙ Uniprot:O75506 ∙ 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 HSBP1 gene.

• not provided (4 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSBP1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	1	0	4

Variants in HSBP1

This is a list of pathogenic ClinVar variants found in the HSBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-83747797-C-T			Benign (Jun 18, 2021)
16-83747999-T-C			Benign (Jun 18, 2021)
16-83748208-G-A		not specified	Uncertain significance (Feb 22, 2023)
16-83748217-G-A		not specified	Uncertain significance (Jul 30, 2023)
16-83748258-C-G		not specified	Likely benign (-)
16-83748314-T-C			Benign (Jun 19, 2021)
16-83748390-A-C			Benign (Jun 18, 2021)
16-83779639-A-G			Benign (Jun 18, 2021)
16-83779689-T-C			Benign (Jun 18, 2021)
16-83779788-G-A			Benign (Jun 18, 2021)
16-83779817-C-T			Benign (Jun 18, 2021)
16-83779906-G-A			Benign (Jun 18, 2021)
16-83779909-A-G			Benign (Jun 18, 2021)
16-83779974-C-T		not specified	Uncertain significance (Jun 12, 2023)
16-83779989-C-G			Uncertain significance (-)
16-83780017-C-T		CDH13-related disorder	Likely benign (Jun 24, 2019)
16-83780035-G-T		CDH13-related disorder	Likely benign (Jul 03, 2019)
16-83780039-A-G		CDH13-related disorder	Uncertain significance (Aug 24, 2022)
16-83780049-C-G		not specified	Uncertain significance (Jan 31, 2022)
16-83780067-A-G		not specified	Uncertain significance (Aug 17, 2022)
16-83780157-A-G		not specified	Uncertain significance (Dec 21, 2022)
16-83780471-T-A			Benign (Jun 18, 2021)
16-83782959-T-C			Benign (Jun 18, 2021)
16-83782974-C-T			Benign (Jun 21, 2021)
16-83783016-T-C			Benign (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSBP1	protein_coding	protein_coding	ENST00000433866	3	11895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.234	0.655	124209	0	2	124211	0.00000805

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	28	38.1	0.734	0.00000201	500
Missense in Polyphen		6	4.4199	1.3575		85
Synonymous	-0.678	17	13.8	1.23	7.40e-7	124
Loss of Function	1.14	1	3.20	0.312	1.36e-7	39

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of the heat shock response. Negatively affects HSF1 DNA-binding activity. May have a role in the suppression of the activation of the stress response during the aging process.
• Pathway: HSF1 activation;Attenuation phase;HSF1-dependent transactivation;Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress (Consensus)

Recessive Scores

• pRec: 0.0915

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

• pHI: 0.142
• hipred: Y
• hipred_score: 0.672
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsbp1
• Phenotype: 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)

Zebrafish Information Network

• Gene name: hsbp1b
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: deformed

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;muscle contraction;endodermal cell differentiation;cellular heat acclimation;regulation of cellular response to heat
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;cytoskeleton
• Molecular function: transcription corepressor activity;protein binding;identical protein binding