HSPA12A

protein-coding

heat shock protein family A (Hsp70) member 12A, the group of Heat shock 70kDa proteins

Gene summary

Predicted to enable ATP binding activity. Predicted to act upstream of or within several processes, including import into nucleus; liver development; and macrophage activation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_025015.3

Inheritance

—

ClinVar variants

U:98B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr10:116,671,192-116,850,251

External References & Databases

Ensembl (ENSG00000165868)

Transcript & Mutation Effects

hg38 • Region Span ~179.1 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 HSPA12A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025015.3. 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			94 clinvar	1 clinvar		95
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	98	2	0	100

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025015.3	RefSeq	NP_079291.2	12	MANE Select
ENST00000369209.8	Ensembl	ENSP00000358211.3	12	MANE Select
NM_001330164.2	RefSeq	NP_001317093.1	13	Standard
ENST00000480802.2	Ensembl	ENSP00000466041.1	2	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

biological_process

Molecular Function

molecular_function
ATP binding

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369209
Coding exons: 12
Length: 71383
Individuals with no LoFs: 124844
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 124853
p: 0.0000360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.12	298	420	0.709	0.0000273	4400
Missense (PolyPhen)		62	113.67	0.54542		1093
Synonymous	0.439	173	181	0.958	0.0000129	1357
Loss of Function	4.42	4	30.3	0.132	0.00000156	344

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.154

Intolerance Scores

LoFtool: 0.391
RVIS EVS: -0.66
RVIS percentile EVS: 15.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.392

Gene Damage Prediction

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