HSPA13

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the heat shock protein 70 family and is found associated with microsomes. Members of this protein family play a role in the processing of cytosolic and secretory proteins, as well as in the removal of denatured or incorrectly-folded proteins. The encoded protein contains an ATPase domain and has been shown to associate with a ubiquitin-like protein. [provided by RefSeq, Jul 2008]

Previous symbols:

STCH

MANE transcript

NM_006948.5

Inheritance

—

ClinVar variants

U:53B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr21:14,371,115-14,383,484

External References & Databases

Ensembl (ENSG00000155304)

Transcript & Mutation Effects

hg38 • Region Span ~12.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HSPA13 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 50

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006948.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			52 clinvar	1 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	1	0	54

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006948.5	RefSeq	NP_008879.3	5	MANE Select
ENST00000285667.4	Ensembl	ENSP00000285667.3	5	MANE Select
ENST00000903931.1	Ensembl	ENSP00000573990.1	4	Standard
ENST00000903931.2	Ensembl	ENSP00000573990.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Regulation of HSF1-mediated heat shock response
Cellular responses to stress
Cellular responses to external stimuli
Cellular response to heat stress

Biological Process

response to unfolded protein
ubiquitin-dependent ERAD pathway
endoplasmic reticulum unfolded protein response
cellular response to heat
cellular response to unfolded protein

Molecular Function

protein binding
ATP binding
ATPase activity
heat shock protein binding
ATPase activity, coupled

Cellular Component

nucleus
cytoplasm
endoplasmic reticulum lumen
membrane
endoplasmic reticulum chaperone complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000285667
Coding exons: 5
Length: 12370
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.24	197	253	0.780	0.0000131	3070
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has peptide-independent ATPase activity.;

Recessive Scores

pRec: 0.143

Intolerance Scores

LoFtool: 0.768
RVIS EVS: -0.16
RVIS percentile EVS: 41.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.895

Gene Damage Prediction

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