SOGA3

SOGA family member 3

Basic information

Region (hg38): 6:127472805-127519335

Previous symbols: [ "C6orf174" ]

Links

ENSG00000214338 ∙ NCBI:387104 ∙ ∙ HGNC:21494 ∙ Uniprot:Q5TF21 ∙ 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 SOGA3 gene.

• Inborn genetic diseases (31 variants)
• not provided (4 variants)
• 7 conditions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOGA3 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					3	3
missense			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	3

Variants in SOGA3

This is a list of pathogenic ClinVar variants found in the SOGA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-127473376-T-C		not specified	Uncertain significance (Mar 07, 2024)
6-127475310-G-A		not specified	Uncertain significance (Jul 14, 2021)
6-127475322-C-T		not specified	Uncertain significance (May 13, 2024)
6-127475340-T-C		not specified	Uncertain significance (May 31, 2023)
6-127475349-C-G		not specified	Uncertain significance (Dec 02, 2022)
6-127475354-C-T		not specified	Uncertain significance (Mar 25, 2024)
6-127475361-T-C		not specified	Uncertain significance (Nov 10, 2022)
6-127475387-G-A		not specified	Uncertain significance (Feb 13, 2025)
6-127475402-T-C		not specified	Uncertain significance (Dec 08, 2024)
6-127475550-C-T		not specified	Uncertain significance (Nov 24, 2024)
6-127475659-G-C		not specified	Uncertain significance (Dec 11, 2023)
6-127475694-C-G		See cases	Uncertain significance (Feb 28, 2025)
6-127475737-G-C		not specified	Uncertain significance (Dec 07, 2023)
6-127475763-T-C		not specified	Uncertain significance (Nov 24, 2024)
6-127475803-G-T		not specified	Uncertain significance (Apr 17, 2024)
6-127475856-A-T		not specified	Uncertain significance (Jan 28, 2025)
6-127475931-C-G		not specified	Uncertain significance (Nov 03, 2022)
6-127475973-C-A		not specified	Uncertain significance (Dec 20, 2023)
6-127475987-T-C		not specified	Uncertain significance (Nov 25, 2024)
6-127476034-G-A			Benign (Dec 23, 2021)
6-127476128-G-A		not specified	Uncertain significance (Nov 08, 2022)
6-127476166-G-T		not specified	Uncertain significance (Aug 20, 2024)
6-127476312-G-C		not specified	Uncertain significance (Dec 21, 2022)
6-127476362-T-C		not specified	Uncertain significance (May 03, 2023)
6-127513004-C-T		not specified	Uncertain significance (Aug 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOGA3	protein_coding	protein_coding	ENST00000556132	6	80950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.679	0.321	124854	0	11	124865	0.0000440

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.32	339	560	0.605	0.0000353	6064
Missense in Polyphen		89	208.38	0.42711		2140
Synonymous	-0.208	258	254	1.02	0.0000184	1944
Loss of Function	4.06	6	30.0	0.200	0.00000129	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000222
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000373	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.59

Haploinsufficiency Scores

• pHI: 0.182
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Soga3

Gene ontology

• Biological process: regulation of autophagy
• Cellular component: extracellular space;integral component of membrane