HSPE1

heat shock protein family E (Hsp10) member 1, the group of Chaperonins

Basic information

Region (hg38): 2:197500140-197503449

Links

ENSG00000115541 ∙ NCBI:3336 ∙ OMIM:600141 ∙ HGNC:5269 ∙ Uniprot:P61604 ∙ 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 HSPE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPE1 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in HSPE1

This is a list of pathogenic ClinVar variants found in the HSPE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-197500319-C-G			Benign (Jun 29, 2018)
2-197500350-A-AT			Likely benign (Jun 29, 2018)
2-197501180-C-G		HSPE1-related condition	Uncertain significance (Sep 13, 2024)
2-197503079-A-C		not specified	Uncertain significance (Feb 08, 2023)
2-197503087-C-T			Uncertain significance (Jul 24, 2019)
2-197503117-C-A		not specified	Uncertain significance (May 29, 2024)
2-197503228-A-T		not specified	Uncertain significance (Feb 12, 2024)
2-197503248-T-C		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPE1	protein_coding	protein_coding	ENST00000233893	4	3464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.804	0.192	125521	0	1	125522	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	23	52.6	0.437	0.00000243	646
Missense in Polyphen		1	4.993	0.20028		86
Synonymous	-1.20	26	19.3	1.35	0.00000102	208
Loss of Function	2.15	0	5.39	0.00	2.30e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Co-chaperonin implicated in mitochondrial protein import and macromolecular assembly. Together with Hsp60, facilitates the correct folding of imported proteins. May also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix (PubMed:7912672, PubMed:1346131, PubMed:11422376). The functional units of these chaperonins consist of heptameric rings of the large subunit Hsp60, which function as a back-to-back double ring. In a cyclic reaction, Hsp60 ring complexes bind one unfolded substrate protein per ring, followed by the binding of ATP and association with 2 heptameric rings of the co-chaperonin Hsp10. This leads to sequestration of the substrate protein in the inner cavity of Hsp60 where, for a certain period of time, it can fold undisturbed by other cell components. Synchronous hydrolysis of ATP in all Hsp60 subunits results in the dissociation of the chaperonin rings and the release of ADP and the folded substrate protein (Probable). {ECO:0000269|PubMed:11422376, ECO:0000269|PubMed:1346131, ECO:0000269|PubMed:7912672, ECO:0000305|PubMed:25918392}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.507

Intolerance Scores

• loftool: 0.393
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.654
• hipred: Y
• hipred_score: 0.656
• ghis: 0.540

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Hspe1

Gene ontology

• Biological process: osteoblast differentiation;protein folding;activation of cysteine-type endopeptidase activity involved in apoptotic process;response to unfolded protein;chaperone cofactor-dependent protein refolding
• Cellular component: mitochondrion;mitochondrial matrix;membrane;extracellular exosome
• Molecular function: RNA binding;protein binding;ATP binding;metal ion binding;unfolded protein binding;chaperone binding