SGTB

small glutamine rich tetratricopeptide repeat co-chaperone beta, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 5:65665928-65723035

Links

ENSG00000197860 ∙ NCBI:54557 ∙ ∙ HGNC:23567 ∙ Uniprot:Q96EQ0 ∙ 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 SGTB gene.

Variants pathogenicity by type

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

Variants in SGTB

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

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

Position	Type	Phenotype	Significance	ClinVar
5-65671975-G-C		not specified	Uncertain significance (May 20, 2024)
5-65672280-G-A		not specified	Uncertain significance (Dec 06, 2021)
5-65685369-C-T		not specified	Uncertain significance (Nov 21, 2023)
5-65704375-T-C		not specified	Uncertain significance (Feb 17, 2023)
5-65708519-C-T		not specified	Uncertain significance (Jul 05, 2024)
5-65712975-T-C		not specified	Uncertain significance (May 02, 2024)
5-65720746-A-G		not specified	Uncertain significance (May 13, 2024)
5-65720791-T-C		not specified	Uncertain significance (Nov 19, 2024)
5-65720794-T-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGTB	protein_coding	protein_coding	ENST00000381007	10	57108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0407	0.958	125734	0	7	125741	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	89	162	0.550	0.00000789	2016
Missense in Polyphen		17	42.421	0.40074		557
Synonymous	1.42	40	53.2	0.752	0.00000256	533
Loss of Function	2.84	6	19.6	0.307	9.24e-7	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Co-chaperone that binds directly to HSC70 and HSP70 and regulates their ATPase activity. {ECO:0000250}.

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.197
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.688
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgtb

Gene ontology

• Biological process: posttranslational protein targeting to endoplasmic reticulum membrane;ubiquitin-dependent ERAD pathway;positive regulation of chaperone-mediated protein folding
• Cellular component: cytosol;membrane;TRC complex
• Molecular function: protein binding;protein-containing complex scaffold activity