SAE1

SUMO1 activating enzyme subunit 1, the group of Ubiquitin like modifier activating enzymes

Basic information

Region (hg38): 19:47113273-47210636

Links

ENSG00000142230 ∙ NCBI:10055 ∙ OMIM:613294 ∙ HGNC:30660 ∙ Uniprot:Q9UBE0 ∙ 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 SAE1 gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAE1 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					1	1
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	7	2	1

Variants in SAE1

This is a list of pathogenic ClinVar variants found in the SAE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47130961-A-G		not specified	Uncertain significance (Aug 18, 2023)
19-47131010-G-A		not specified	Uncertain significance (Mar 21, 2022)
19-47143522-G-A			Likely benign (Apr 01, 2022)
19-47143562-T-G		not specified	Uncertain significance (Oct 03, 2023)
19-47150242-C-A		not specified	Uncertain significance (Sep 17, 2021)
19-47150257-G-A		not specified	Uncertain significance (Mar 22, 2023)
19-47150262-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-47150323-A-G		not specified	Uncertain significance (Dec 13, 2023)
19-47150340-A-G		not specified	Uncertain significance (Nov 08, 2022)
19-47197285-T-C			Benign (Dec 31, 2019)
19-47197298-G-C		not specified	Uncertain significance (Jan 08, 2024)
19-47203687-A-G		not specified	Uncertain significance (Feb 14, 2024)
19-47203732-A-G		not specified	Uncertain significance (Dec 08, 2023)
19-47209190-A-G		not specified	Uncertain significance (Aug 02, 2021)
19-47209207-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-47209278-G-A			Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAE1	protein_coding	protein_coding	ENST00000270225	9	97356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0124	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.563	170	192	0.886	0.0000101	2267
Missense in Polyphen		38	56.538	0.67212		687
Synonymous	-0.478	77	71.8	1.07	0.00000397	664
Loss of Function	3.67	1	17.7	0.0566	9.29e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000333	0.0000333
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The heterodimer acts as an E1 ligase for SUMO1, SUMO2, SUMO3, and probably SUMO4. It mediates ATP-dependent activation of SUMO proteins followed by formation of a thioester bond between a SUMO protein and a conserved active site cysteine residue on UBA2/SAE2. {ECO:0000269|PubMed:10187858, ECO:0000269|PubMed:10217437, ECO:0000269|PubMed:11451954, ECO:0000269|PubMed:11481243, ECO:0000269|PubMed:15660128, ECO:0000269|PubMed:20164921, ECO:0000269|PubMed:9920803}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);er associated degradation (erad) pathway;SUMO is conjugated to E1 (UBA2:SAE1);SUMO is transferred from E1 to E2 (UBE2I, UBC9);Post-translational protein modification;basic mechanisms of sumoylation;Metabolism of proteins;Processing and activation of SUMO;SUMOylation (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.449
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.632
• hipred: Y
• hipred_score: 0.831
• ghis: 0.662

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sae1

Zebrafish Information Network

• Gene name: sae1
• Affected structure: hematopoietic multipotent progenitor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein ubiquitination;protein sumoylation;protein modification by small protein conjugation;positive regulation of catalytic activity;positive regulation of protein targeting to mitochondrion
• Cellular component: nucleus;nucleoplasm;cytoplasm;SUMO activating enzyme complex
• Molecular function: ubiquitin activating enzyme activity;protein binding;protein C-terminus binding;enzyme activator activity;SUMO activating enzyme activity;ATP-dependent protein binding;small protein activating enzyme binding;protein heterodimerization activity