SGTA

protein-coding

small glutamine rich tetratricopeptide repeat co-chaperone alpha, the group of Tetratricopeptide repeat domain containing|GET4-GET5 transmembrane domain recognition complex subunits

Gene summary

This gene encodes a protein which is capable of interacting with the major nonstructural protein of parvovirus H-1 and 70-kDa heat shock cognate protein; however, its function is not known. Since this transcript is expressed ubiquitously in various tissues, this protein may serve a housekeeping function. [provided by RefSeq, Jul 2008]

Previous symbols:

MANE transcript

NM_003021.4

Inheritance

—

ClinVar variants

U:28B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr19:2,754,715-2,783,362

External References & Databases

Ensembl (ENSG00000104969)

Transcript & Mutation Effects

hg38 • Region Span ~28.6 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 SGTA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 18

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003021.4. 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	1 clinvar	2 clinvar	5
missense			18 clinvar			18
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	28	1	2	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003021.4	RefSeq	NP_003012.1	10	MANE Select
ENST00000221566.7	Ensembl	ENSP00000221566.1	10	MANE Select
ENST00000587866.1	Ensembl	ENSP00000468443.1	2	Standard
ENST00000589251.5	Ensembl	ENSP00000466461.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

posttranslational protein targeting to endoplasmic reticulum membrane
viral process
ubiquitin-dependent ERAD pathway
chaperone-mediated protein folding
tail-anchored membrane protein insertion into ER membrane

Molecular Function

protein binding
protein-containing complex scaffold activity
identical protein binding
protein self-association
BAT3 complex binding

Cellular Component

nucleus
cytoplasm
cytosol
membrane
TRC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000221566
Coding exons: 10
Length: 28658
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125726
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.97	131	212	0.619	0.0000142	2058
Missense (PolyPhen)		24	62.477	0.38414		677
Synonymous	-0.283	99	95.5	1.04	0.00000789	572
Loss of Function	3.50	2	18.0	0.111	8.66e-7	201

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000060	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Co-chaperone that binds misfolded and hydrophobic patches-containing client proteins in the cytosol. Mediates their targeting to the endoplasmic reticulum but also regulates their sorting to the proteasome when targeting fails (PubMed:28104892). Functions in tail-anchored/type II transmembrane proteins membrane insertion constituting with ASNA1 and the BAG6 complex a targeting module (PubMed:28104892). Functions upstream of the BAG6 complex and ASNA1, binding more rapidly the transmembrane domain of newly synthesized proteins (PubMed:28104892, PubMed:25535373). It is also involved in the regulation of the endoplasmic reticulum- associated misfolded protein catabolic process via its interaction with BAG6: collaborates with the BAG6 complex to maintain hydrophobic substrates in non-ubiquitinated states (PubMed:23129660, PubMed:25179605). Competes with RNF126 for interaction with BAG6, preventing the ubiquitination of client proteins associated with the BAG6 complex (PubMed:27193484). Binds directly to HSC70 and HSP70 and regulates their ATPase activity (PubMed:18759457). {ECO:0000269|PubMed:18759457, ECO:0000269|PubMed:23129660, ECO:0000269|PubMed:25179605, ECO:0000269|PubMed:25535373, ECO:0000269|PubMed:27193484, ECO:0000269|PubMed:28104892}.;

Recessive Scores

pRec: 0.249

Intolerance Scores

LoFtool: 0.0715
RVIS EVS: -0.67
RVIS percentile EVS: 15.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.977

Gene Damage Prediction

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