HSPA12A

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

Basic information

Region (hg38): 10:116671192-116850251

Links

ENSG00000165868 ∙ NCBI:259217 ∙ OMIM:610701 ∙ HGNC:19022 ∙ Uniprot:O43301 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HSPA12A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPA12A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	38	1	0

Variants in HSPA12A

This is a list of pathogenic ClinVar variants found in the HSPA12A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-116674797-T-G		not specified	Uncertain significance (Mar 25, 2024)
10-116674830-A-G		not specified	Uncertain significance (Dec 16, 2022)
10-116674831-T-C		not specified	Uncertain significance (Feb 28, 2024)
10-116674864-C-T		not specified	Uncertain significance (Sep 06, 2022)
10-116674960-C-T		not specified	Uncertain significance (May 20, 2024)
10-116674987-C-T		not specified	Uncertain significance (Apr 15, 2024)
10-116675052-C-T		not specified	Uncertain significance (Sep 26, 2023)
10-116675110-C-T		not specified	Uncertain significance (Nov 08, 2022)
10-116675125-G-A		not specified	Uncertain significance (Apr 28, 2022)
10-116675157-G-A		not specified	Uncertain significance (Jun 18, 2024)
10-116675188-C-T		not specified	Uncertain significance (Aug 04, 2023)
10-116675233-C-T		not specified	Uncertain significance (Apr 25, 2022)
10-116675239-C-A		not specified	Uncertain significance (Jan 06, 2023)
10-116675301-C-T		not specified	Uncertain significance (Dec 21, 2022)
10-116675347-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-116675353-C-T		not specified	Uncertain significance (Mar 06, 2023)
10-116675398-C-T		not specified	Uncertain significance (Sep 23, 2023)
10-116676418-A-T		not specified	Uncertain significance (May 23, 2023)
10-116676440-G-A		not specified	Uncertain significance (Mar 16, 2022)
10-116676441-C-T		not specified	Uncertain significance (Feb 13, 2024)
10-116679656-G-C		not specified	Uncertain significance (Oct 20, 2023)
10-116679694-C-A		not specified	Uncertain significance (Sep 30, 2021)
10-116679723-C-T		not specified	Uncertain significance (Jul 25, 2023)
10-116681218-C-T		not specified	Uncertain significance (Dec 05, 2022)
10-116681241-A-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPA12A	protein_coding	protein_coding	ENST00000369209	12	71383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0156	124844	0	9	124853	0.0000360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	298	420	0.709	0.0000273	4400
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000444	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Regulation of HSF1-mediated heat shock response;Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.391
• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.95

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.809
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.392

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hspa12a

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular exosome
• Molecular function: molecular_function;ATP binding