SOGA1

suppressor of glucose, autophagy associated 1

Basic information

Region (hg38): 20:36777446-36863538

Previous symbols: [ "C20orf117", "KIAA0889" ]

Links

ENSG00000149639 ∙ NCBI:140710 ∙ OMIM:620225 ∙ HGNC:16111 ∙ Uniprot:O94964 ∙ 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 SOGA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOGA1 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				4	1	5
missense			110	5	1	116
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	111	9	2

Variants in SOGA1

This is a list of pathogenic ClinVar variants found in the SOGA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36786495-G-T		not specified	Uncertain significance (Jun 22, 2021)
20-36786496-G-T		not specified	Uncertain significance (Oct 08, 2024)
20-36786499-G-T		not specified	Uncertain significance (Dec 02, 2024)
20-36786541-G-A		not specified	Uncertain significance (Sep 28, 2021)
20-36786567-C-T		not specified	Uncertain significance (Nov 02, 2021)
20-36786580-G-A		not specified	Uncertain significance (May 08, 2023)
20-36786588-C-T		not specified	Uncertain significance (Nov 24, 2024)
20-36786592-C-T		not specified	Uncertain significance (Dec 09, 2024)
20-36786603-G-T		not specified	Uncertain significance (Jun 05, 2023)
20-36786607-G-A		not specified	Uncertain significance (Jan 07, 2025)
20-36786634-C-T		not specified	Uncertain significance (Mar 03, 2025)
20-36793253-T-C		not specified	Likely benign (Feb 17, 2023)
20-36793257-G-T		not specified	Uncertain significance (Sep 10, 2024)
20-36793283-C-T		not specified	Uncertain significance (Nov 10, 2022)
20-36793305-C-T		not specified	Uncertain significance (Apr 13, 2022)
20-36793397-T-C		not specified	Uncertain significance (Nov 10, 2022)
20-36793416-G-C		not specified	Uncertain significance (Aug 02, 2021)
20-36793473-C-G		not specified	Uncertain significance (Dec 01, 2022)
20-36793574-C-T		not specified	Uncertain significance (Jan 17, 2025)
20-36793674-C-T		not specified	Uncertain significance (Aug 17, 2022)
20-36793742-C-T		not specified	Uncertain significance (Jul 12, 2022)
20-36793788-G-C		not specified	Uncertain significance (Mar 04, 2024)
20-36793799-G-A		not specified	Uncertain significance (Dec 05, 2024)
20-36793810-G-C		not specified	Uncertain significance (Jun 07, 2024)
20-36793874-G-A		not specified	Uncertain significance (Jan 09, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOGA1	protein_coding	protein_coding	ENST00000237536	15	86245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000448	125171	0	19	125190	0.0000759

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	721	914	0.789	0.0000612	10549
Missense in Polyphen		281	411.1	0.68354		4527
Synonymous	1.23	368	399	0.922	0.0000271	3420
Loss of Function	6.52	6	60.9	0.0985	0.00000320	725

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000947	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.000234	0.000222
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000101	0.0000971
Middle Eastern	0.000234	0.000222
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates autophagy by playing a role in the reduction of glucose production in an adiponectin- and insulin-dependent manner. {ECO:0000250}.

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.448
• hipred: Y
• hipred_score: 0.662
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Soga1

Gene ontology

• Biological process: insulin receptor signaling pathway;regulation of autophagy;negative regulation of gluconeogenesis
• Cellular component: extracellular space;extracellular exosome
• Molecular function: molecular_function