HSPA12B

protein-coding

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

Gene summary

The protein encoded by this gene contains an atypical heat shock protein 70 (Hsp70) ATPase domain and is therefore a distant member of the mammalian Hsp70 family. This gene may be involved in susceptibility to atherosclerosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

Previous symbols:

C20orf60

MANE transcript

NM_052970.5

Inheritance

—

ClinVar variants

U:104B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr20:3,732,685-3,753,111

External References & Databases

Ensembl (ENSG00000132622)

Transcript & Mutation Effects

hg38 • Region Span ~20.4 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 HSPA12B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 103

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052970.5. 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			2 clinvar	4 clinvar		6
missense			100 clinvar	3 clinvar	2 clinvar	105
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	104	7	2	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 74 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052970.5	RefSeq	NP_443202.3	12	MANE Select
ENST00000254963.7	Ensembl	ENSP00000254963.2	12	MANE Select
NM_001197327.2	RefSeq	NP_001184256.1	12	Standard
NM_001318322.2	RefSeq	NP_001305251.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
hspa12b	Danio rerio	Structure: pectoral fin blood vessel Quality: decreased width abnormal

Gene / Model

Organism

Observed Phenotype

hspa12b

Danio rerio

Structure: pectoral fin blood vessel

Quality: decreased width

abnormal

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

Molecular Function

protein binding
ATP binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254963
Coding exons: 12
Length: 20445
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125747
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.27	295	427	0.690	0.0000283	4315
Missense (PolyPhen)		76	126.84	0.5992		1310
Synonymous	1.89	157	190	0.825	0.0000134	1450
Loss of Function	3.15	11	29.5	0.373	0.00000152	312

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00070	0.00069	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000071	0.000062	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.121

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.104

Gene Damage Prediction

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