HSPBP1

HSPA (Hsp70) binding protein 1, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 19:55262222-55280381

Links

ENSG00000133265 ∙ NCBI:23640 ∙ OMIM:612939 ∙ HGNC:24989 ∙ Uniprot:Q9NZL4 ∙ 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 HSPBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPBP1 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				3	1	4
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	24	4	2

Variants in HSPBP1

This is a list of pathogenic ClinVar variants found in the HSPBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55262626-G-C		not specified	Uncertain significance (Feb 27, 2023)
19-55265309-C-A		not specified	Uncertain significance (May 23, 2024)
19-55265312-C-T		not specified	Uncertain significance (May 07, 2024)
19-55265345-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-55265385-C-A			Likely benign (Jun 08, 2018)
19-55265934-C-T		not specified	Uncertain significance (Jun 05, 2024)
19-55265956-G-C		not specified	Uncertain significance (May 22, 2023)
19-55265971-A-T		not specified	Uncertain significance (Apr 25, 2023)
19-55266200-C-G		not specified	Uncertain significance (Nov 12, 2021)
19-55266248-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-55266259-A-G		not specified	Uncertain significance (Oct 10, 2023)
19-55274407-C-A		not specified	Uncertain significance (May 26, 2022)
19-55274416-C-T		not specified	Uncertain significance (May 25, 2022)
19-55274422-C-T		not specified	Uncertain significance (Jun 21, 2021)
19-55274424-C-T		not specified	Uncertain significance (May 20, 2024)
19-55274425-G-A		not specified	Uncertain significance (Dec 21, 2022)
19-55274444-G-A			Likely benign (Jul 20, 2018)
19-55274469-C-T		not specified	Uncertain significance (May 04, 2023)
19-55274470-G-T		not specified	Uncertain significance (Mar 15, 2024)
19-55274512-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-55274526-G-A		not specified	Uncertain significance (Feb 23, 2023)
19-55274563-C-T		not specified	Uncertain significance (Oct 25, 2023)
19-55274583-C-T		not specified	Uncertain significance (Mar 24, 2023)
19-55274594-C-T			Likely benign (Dec 20, 2017)
19-55277693-C-G		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPBP1	protein_coding	protein_coding	ENST00000255631	7	18151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0572	0.939	125695	0	27	125722	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	182	226	0.805	0.0000142	2250
Missense in Polyphen		54	66.364	0.81369		635
Synonymous	0.135	100	102	0.983	0.00000647	757
Loss of Function	2.57	5	16.1	0.310	8.35e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000274
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000182	0.000167
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits HSPA1A chaperone activity by changing the conformation of the ATP-binding domain of HSPA1A and interfering with ATP binding. Interferes with ubiquitination mediated by STUB1 and inhibits chaperone-assisted degradation of immature CFTR. {ECO:0000269|PubMed:10786638, ECO:0000269|PubMed:12651857, ECO:0000269|PubMed:15215316, ECO:0000269|PubMed:9830037}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.649
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.553
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hspbp1
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: protein folding;positive regulation of protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of catalytic activity
• Cellular component: cytoplasm;endoplasmic reticulum
• Molecular function: adenyl-nucleotide exchange factor activity;enzyme inhibitor activity;protein binding;ubiquitin protein ligase binding