HSPA12B

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

Basic information

Region (hg38): 20:3732685-3753111

Previous symbols: [ "C20orf60" ]

Links

ENSG00000132622 ∙ NCBI:116835 ∙ OMIM:610702 ∙ HGNC:16193 ∙ Uniprot:Q96MM6 ∙ 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 HSPA12B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPA12B 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				2		2
missense			45	2	1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	4	1

Variants in HSPA12B

This is a list of pathogenic ClinVar variants found in the HSPA12B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3740830-G-A		not specified	Uncertain significance (Feb 28, 2023)
20-3740833-C-T		not specified	Uncertain significance (Dec 14, 2021)
20-3740838-G-C			Benign (Apr 24, 2018)
20-3740841-C-G		not specified	Uncertain significance (Jun 22, 2023)
20-3740860-C-T		not specified	Uncertain significance (Dec 19, 2022)
20-3740880-G-A		not specified	Uncertain significance (Jul 26, 2022)
20-3740887-C-T		not specified	Uncertain significance (May 10, 2022)
20-3740898-C-A		not specified	Uncertain significance (Jul 20, 2021)
20-3742294-T-C		not specified	Likely benign (May 31, 2023)
20-3742297-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-3742315-C-T		not specified	Uncertain significance (Nov 09, 2023)
20-3744912-G-A		not specified	Uncertain significance (Mar 20, 2023)
20-3744943-C-T		not specified	Uncertain significance (Sep 17, 2021)
20-3744945-C-G		not specified	Uncertain significance (Sep 26, 2023)
20-3744946-C-T		not specified	Uncertain significance (Sep 17, 2021)
20-3744986-C-T			Likely benign (Sep 12, 2018)
20-3745047-C-T		not specified	Uncertain significance (Sep 07, 2022)
20-3745060-A-T		not specified	Uncertain significance (Oct 13, 2023)
20-3745937-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-3745987-T-C		not specified	Uncertain significance (Feb 16, 2023)
20-3745996-C-T		not specified	Uncertain significance (Jan 26, 2022)
20-3748292-C-T		not specified	Uncertain significance (Dec 20, 2022)
20-3748302-G-A		not specified	Uncertain significance (Jun 24, 2022)
20-3748326-G-A		not specified	Uncertain significance (May 29, 2024)
20-3749265-G-A		not specified	Uncertain significance (Mar 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPA12B	protein_coding	protein_coding	ENST00000254963	12	20445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000453	0.999	125723	0	24	125747	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	295	427	0.690	0.0000283	4315
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000148
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.0000545	0.0000544
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000713	0.0000615
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000985	0.0000980
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: 0.121

Haploinsufficiency Scores

• pHI: 0.131
• hipred: Y
• hipred_score: 0.623
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.104

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hspa12b

Zebrafish Information Network

• Gene name: hspa12b
• Affected structure: pectoral fin blood vessel
• Phenotype tag: abnormal
• Phenotype quality: decreased width

Gene ontology

• Molecular function: protein binding;ATP binding