HSPD1

Chr 2

heat shock protein family D (Hsp60) member 1

Also known as: CPN60, GROEL, HLD4, HSP-60, HSP60, HSP65, HuCHA60, SPG13

NCBI Gene: 3329ENSG00000144381UniProt: P10809

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]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtSpastic paraplegia 13, autosomal dominant
UniProtLeukodystrophy, hypomyelinating, 4

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
59
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.27
LOEUF· LoF intol.
LOF
Mechanism· G2P
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GeneReview available — HSPD1
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.27LOEUF
pLI 0.993
Z-score 4.11
OE 0.09 (0.03–0.27)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
2.26Z-score
OE missense 0.64 (0.57–0.72)
195 obs / 306.1 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.09 (0.03–0.27)
0≤0.351.4
Missense OE?0.64 (0.57–0.72)
0≤0.61.4
Synonymous OE?1.00
0≤1.21.6
LoF obs/exp: 2 / 23.5Missense obs/exp: 195 / 306.1Syn Z: -0.01

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

HSPD1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients