HSPD1

protein-coding

heat shock protein family D (Hsp60) member 1, the group of Chaperonins

Gene summary

This gene encodes a member of the chaperonin family. The encoded mitochondrial protein may function as a signaling molecule in the innate immune system. This protein is essential for the folding and assembly of newly imported proteins in the mitochondria. This gene is adjacent to a related family member and the region between the 2 genes functions as a bidirectional promoter. Several pseudogenes have been associated with this gene. Two transcript variants encoding the same protein have been identified for this gene. Mutations associated with this gene cause autosomal recessive spastic paraplegia 13. [provided by RefSeq, Jun 2010]

Previous symbols:
  • SPG13

MANE transcript

NM_002156.5

Inheritance

AR, AD

ClinVar variants

P:10U:181B:76

Top phenotype

Spastic paraplegia 13, autosomal dominant; Leukodystrophy, hypomyelinating, 4

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr2:197,486,584-197,516,737

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~30.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

leukodystrophy, hypomyelinating, 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012824

Submitter: G2P

hereditary spastic paraplegia 13MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0011532

Submitter: Ambry Genetics

leukodystrophy, hypomyelinating, 4LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0012824

Submitter: Ambry Genetics

hereditary spastic paraplegia 13STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011532

Submitter: Labcorp Genetics (formerly Invitae)

leukodystrophy, hypomyelinating, 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012824

Submitter: Labcorp Genetics (formerly Invitae)

leukodystrophy, hypomyelinating, 4SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012824

Submitter: Orphanet

hereditary spastic paraplegia 13SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011532

Submitter: Orphanet

hereditary spastic paraplegia 13STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011532

Submitter: PanelApp Australia

leukodystrophy, hypomyelinating, 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012824

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Spastic paraplegia 13, autosomal dominant; Leukodystrophy, hypomyelinating, 4AD/AR

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 10677329; 11898127; 17420924; 18571143Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HSPD1 variants in ClinVar

11 Conditions Cataloged
Spastic paraplegiaTotal: 215
not providedTotal: 85
not specifiedTotal: 48
Hereditary spastic paraplegia 13Total: 41
Inborn genetic diseasesTotal: 32
Hereditary spastic paraplegiaTotal: 19
Leukodystrophy, hypomyelinating, 4Total: 17
HSPD1-related disorderTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002156.5. 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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
64
clinvar
5
clinvar
76
missense
2
clinvar
8
clinvar
162
clinvar
6
clinvar
1
clinvar
179
nonsense
3
clinvar
3
start loss
0
frameshift
3
clinvar
3
splice donor/acceptor (+/-2bp)
6
clinvar
6
Total28181706267

Highest pathogenic variant AF is 0.0000049579935

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 88 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002156.5RefSeqNP_002147.211MANE Select
ENST00000388968.8EnsemblENSP00000373620.311MANE Select
NM_199440.2RefSeqNP_955472.111Standard
ENST00000345042.6EnsemblENSP00000340019.211Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
hspd1Danio rerio

Structure: blastema

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Type I diabetes mellitus - Homo sapiens (human)
  • Legionellosis - Homo sapiens (human)
  • RNA degradation - Homo sapiens (human)
  • Tuberculosis - Homo sapiens (human)
  • Apoptosis-related network due to altered Notch3 in ovarian cancer

Biological Process

  • response to hypoxia
  • B cell cytokine production
  • MyD88-dependent toll-like receptor signaling pathway
  • positive regulation of T cell mediated immune response to tumor cell
  • response to ischemia

Molecular Function

  • lipopolysaccharide binding
  • protease binding
  • p53 binding
  • DNA replication origin binding
  • single-stranded DNA binding

Cellular Component

  • extracellular space
  • cytoplasm
  • mitochondrion
  • mitochondrial inner membrane
  • mitochondrial matrix

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000388968
Coding exons
11
Length
30157
Individuals with no LoFs
125743
Homozygous LoFs
0
Heterozygous LoFs
5
Defined
125748
p
0.0000199
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.261953060.6370.00001503736
Missense (PolyPhen)3387.6170.376641246
Synonymous-0.008991011011.000.000005011143
Loss of Function4.11223.50.08530.00000118317

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000350.000035rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Chaperonin implicated in mitochondrial protein import and macromolecular assembly. Together with Hsp10, 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: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:0000305|PubMed:25918392}.;
Disease
DISEASE: Spastic paraplegia 13, autosomal dominant (SPG13) [MIM:605280]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269|PubMed:11898127}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leukodystrophy, hypomyelinating, 4 (HLD4) [MIM:612233]: A severe autosomal recessive hypomyelinating leukodystrophy. Clinically characterized by infantile-onset rotary nystagmus, progressive spastic paraplegia, neurologic regression, motor impairment, profound mental retardation. Death usually occurs within the first two decades of life. {ECO:0000269|PubMed:18571143}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.981

Intolerance Scores

LoFtool
0.419
RVIS EVS
-0.2
RVIS percentile EVS
38.82

Essentials

Essential (CRISPR)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.941

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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