HSPA13

heat shock protein family A (Hsp70) member 13, the group of Heat shock 70kDa proteins

Basic information

Region (hg38): 21:14371115-14383484

Previous symbols: [ "STCH" ]

Links

ENSG00000155304 ∙ NCBI:6782 ∙ OMIM:601100 ∙ HGNC:11375 ∙ Uniprot:P48723 ∙ 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 HSPA13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPA13 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in HSPA13

This is a list of pathogenic ClinVar variants found in the HSPA13 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-14373691-C-T		not specified	Uncertain significance (Apr 18, 2023)
21-14373747-G-T		not specified	Uncertain significance (Nov 03, 2023)
21-14373904-G-A		not specified	Uncertain significance (Dec 02, 2022)
21-14373931-T-G		not specified	Uncertain significance (Jun 29, 2023)
21-14373993-C-T		not specified	Likely benign (Mar 30, 2022)
21-14373994-G-A		not specified	Uncertain significance (Dec 15, 2022)
21-14373996-C-T		not specified	Uncertain significance (Aug 03, 2022)
21-14374041-T-A		not specified	Uncertain significance (Oct 26, 2021)
21-14374120-C-G		not specified	Uncertain significance (Jan 29, 2024)
21-14374120-C-T		not specified	Uncertain significance (Oct 13, 2023)
21-14374173-C-T		not specified	Uncertain significance (Sep 26, 2024)
21-14375715-C-T		not specified	Uncertain significance (Sep 26, 2022)
21-14375736-A-T		not specified	Uncertain significance (Oct 12, 2024)
21-14378320-C-G		not specified	Uncertain significance (Feb 16, 2023)
21-14378330-C-T		not specified	Uncertain significance (Jan 03, 2022)
21-14378357-G-A		not specified	Uncertain significance (Apr 25, 2023)
21-14381216-C-T		not specified	Uncertain significance (Oct 26, 2022)
21-14381244-C-T		not specified	Uncertain significance (Jul 08, 2022)
21-14381315-A-G		not specified	Uncertain significance (Mar 08, 2024)
21-14381316-C-T		not specified	Uncertain significance (Jul 15, 2021)
21-14381318-C-T		not specified	Uncertain significance (Mar 01, 2023)
21-14381349-T-A		not specified	Uncertain significance (May 08, 2023)
21-14381394-G-C		not specified	Uncertain significance (Feb 15, 2023)
21-14381420-G-A		not specified	Uncertain significance (Nov 24, 2024)
21-14383110-C-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPA13	protein_coding	protein_coding	ENST00000285667	5	12370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0169	0.979	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	197	253	0.780	0.0000131	3070
Missense in Polyphen		69	117.43	0.58757		1449
Synonymous	0.707	87	95.8	0.908	0.00000511	943
Loss of Function	2.50	6	17.2	0.350	8.78e-7	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000114
Middle Eastern	0.000326	0.000326
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has peptide-independent ATPase activity.
• Pathway: Regulation of HSF1-mediated heat shock response;Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.768
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.244
• hipred: N
• hipred_score: 0.282
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hspa13

Gene ontology

• Biological process: response to unfolded protein;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;cellular response to heat;cellular response to unfolded protein;protein refolding;chaperone cofactor-dependent protein refolding
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum lumen;membrane;endoplasmic reticulum chaperone complex;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;ATP binding;ATPase activity;heat shock protein binding;ATPase activity, coupled;protein folding chaperone;unfolded protein binding;misfolded protein binding