SIAE

sialic acid acetylesterase

Basic information

Region (hg38): 11:124633112-124695707

Previous symbols: [ "YSG2" ]

Links

ENSG00000110013 ∙ NCBI:54414 ∙ OMIM:610079 ∙ HGNC:18187 ∙ Uniprot:Q9HAT2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autoimmune disease, susceptibility to, 6 (Limited), mode of inheritance: Unknown
• autoimmune disease, susceptibility to, 6 (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SIAE gene.

• not provided (304 variants)
• Inborn genetic diseases (25 variants)
• Autoimmune disease, susceptibility to, 6 (4 variants)
• SIAE-related condition (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIAE 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	54	8	65
missense			143	5	9	157
nonsense			8			8
start loss			6			6
frameshift			13			13
inframe indel			5			5
splice donor/acceptor (+/-2bp)			6			6
splice region			7	1	1	9
non coding			7	36	4	47
Total	0	0	191	95	21

Variants in SIAE

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

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

Position	Type	Phenotype	Significance	ClinVar
11-124636979-G-A		not specified	Uncertain significance (Jul 06, 2022)
11-124636981-A-G			Likely benign (Sep 15, 2022)
11-124636988-T-A			Uncertain significance (Feb 17, 2021)
11-124637003-A-C			Uncertain significance (Jan 04, 2024)
11-124637008-GGGA-G			Uncertain significance (Aug 21, 2022)
11-124637031-T-G			Uncertain significance (Dec 15, 2023)
11-124637032-G-T			Likely benign (Aug 23, 2023)
11-124637039-T-TA			Uncertain significance (Jun 15, 2022)
11-124637041-T-C			Benign (Jan 19, 2024)
11-124637044-G-A			Likely benign (Oct 27, 2023)
11-124637047-A-G			Likely benign (Apr 12, 2023)
11-124637051-T-C			Uncertain significance (Aug 04, 2023)
11-124637059-T-C			Likely benign (Jan 18, 2022)
11-124637059-T-G			Uncertain significance (Jun 29, 2022)
11-124637068-C-T			Uncertain significance (Jan 07, 2022)
11-124637071-C-T		SIAE-related disorder	Benign (Jan 31, 2024)
11-124637072-G-A			Uncertain significance (Dec 08, 2022)
11-124637074-G-A			Likely benign (Jul 19, 2022)
11-124637080-A-G			Likely benign (Apr 10, 2023)
11-124637083-A-G			Likely benign (Jun 23, 2023)
11-124637087-C-T			Uncertain significance (Aug 30, 2023)
11-124637088-G-A			Uncertain significance (Dec 27, 2023)
11-124637093-G-A			Uncertain significance (Dec 08, 2022)
11-124637098-C-T			Uncertain significance (Jan 12, 2022)
11-124637100-C-T			Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIAE	protein_coding	protein_coding	ENST00000263593	10	62595

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.79e-12	0.248	125640	1	107	125748	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.125	281	287	0.979	0.0000163	3411
Missense in Polyphen		68	91.487	0.74328		1052
Synonymous	-0.780	119	109	1.10	0.00000633	1028
Loss of Function	0.939	20	25.1	0.798	0.00000123	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00154	0.00154
Ashkenazi Jewish	0.00	0.00
East Asian	0.00152	0.00152
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000246	0.000246
Middle Eastern	0.00152	0.00152
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the removal of O-acetyl ester groups from position 9 of the parent sialic acid, N-acetylneuraminic acid.

Recessive Scores

• pRec: 0.195

Intolerance Scores

• loftool: 0.208
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.229
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Siae
• Phenotype: immune system phenotype; renal/urinary system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of immune system process;carbohydrate metabolic process
• Cellular component: extracellular space;lysosome;extracellular exosome
• Molecular function: sialate O-acetylesterase activity