BAG2

BAG cochaperone 2, the group of BAG cochaperones

Basic information

Region (hg38): 6:57172325-57189833

Links

ENSG00000112208 ∙ NCBI:9532 ∙ OMIM:603882 ∙ HGNC:938 ∙ Uniprot:O95816 ∙ 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 BAG2 gene.

• RAB23-related Carpenter syndrome (33 variants)
• Carpenter syndrome (5 variants)
• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAG2 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			27	5	6	38
Total	0	0	30	5	6

Variants in BAG2

This is a list of pathogenic ClinVar variants found in the BAG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-57172789-G-T		not specified	Uncertain significance (Oct 27, 2021)
6-57182140-C-T			Uncertain significance (Feb 01, 2019)
6-57183918-A-G		not specified	Uncertain significance (Aug 01, 2022)
6-57183946-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-57187131-T-C		RAB23-related Carpenter syndrome	Benign (Jan 13, 2018)
6-57187163-T-C		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57187272-A-G		RAB23-related Carpenter syndrome	Likely benign (Jan 13, 2018)
6-57187332-C-G		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57187428-G-A		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57187585-A-G		RAB23-related Carpenter syndrome	Uncertain significance (Jan 12, 2018)
6-57187692-G-T		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57187708-C-T		RAB23-related Carpenter syndrome	Uncertain significance (Feb 09, 2018)
6-57187780-C-T		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57187875-C-T		RAB23-related Carpenter syndrome	Uncertain significance (Jan 12, 2018)
6-57187976-T-C		RAB23-related Carpenter syndrome	Benign (Jan 12, 2018)
6-57188036-C-T		RAB23-related Carpenter syndrome	Benign (Jan 13, 2018)
6-57188120-G-T		RAB23-related Carpenter syndrome	Uncertain significance (Jan 12, 2018)
6-57188142-A-G		RAB23-related Carpenter syndrome	Uncertain significance (Jan 12, 2018)
6-57188188-A-G		RAB23-related Carpenter syndrome	Benign (Jan 13, 2018)
6-57188216-A-G		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57188394-T-C		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57188453-C-T		RAB23-related Carpenter syndrome	Uncertain significance (Jan 13, 2018)
6-57188644-T-C		RAB23-related Carpenter syndrome	Uncertain significance (Jan 12, 2018)
6-57188721-G-A		RAB23-related Carpenter syndrome	Benign (Jan 12, 2018)
6-57188755-A-G		RAB23-related Carpenter syndrome	Likely benign (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BAG2	protein_coding	protein_coding	ENST00000370693	3	17508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0420	0.856	125697	0	16	125713	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	68	105	0.648	0.00000488	1389
Missense in Polyphen		13	28.108	0.4625		380
Synonymous	0.814	32	38.4	0.833	0.00000183	396
Loss of Function	1.33	3	6.72	0.446	2.80e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000631	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000795	0.0000792
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Co-chaperone for HSP70 and HSC70 chaperone proteins. Acts as a nucleotide-exchange factor (NEF) promoting the release of ADP from the HSP70 and HSC70 proteins thereby triggering client/substrate protein release (PubMed:24318877, PubMed:9873016). {ECO:0000269|PubMed:24318877, ECO:0000269|PubMed:9873016}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);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: 0.173

Intolerance Scores

• loftool: 0.458
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.232
• hipred: Y
• hipred_score: 0.716
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bag2

Gene ontology

• Biological process: protein folding;positive regulation of protein processing;protein metabolic process;negative regulation of protein ubiquitination;negative regulation of protein binding;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;protein stabilization;regulation of cellular response to heat;positive regulation of proteasomal protein catabolic process;negative regulation of ubiquitin protein ligase activity
• Cellular component: cytosol;microtubule;axon;dendrite;chaperone complex;dendritic microtubule
• Molecular function: adenyl-nucleotide exchange factor activity;protein binding;heat shock protein binding;ubiquitin protein ligase binding;identical protein binding;ion channel binding;tau protein binding;chaperone binding