SUDS3

SDS3 homolog, SIN3A corepressor complex component, the group of SIN3 histone deacetylase complex subunits

Basic information

Region (hg38): 12:118376555-118418033

Links

ENSG00000111707

∙ NCBI:64426 ∙ OMIM:608250 ∙ HGNC:29545 ∙ Uniprot:Q9H7L9 ∙ 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 SUDS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUDS3 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				2 clinvar		2
missense			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in SUDS3

This is a list of pathogenic ClinVar variants found in the SUDS3 region.

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

Position	Phenotype	Significance	ClinVar
12-118376700-C-T		Likely benign (Apr 01, 2023)	2643381
12-118376784-G-C	not specified	Uncertain significance (Oct 13, 2021)	2223409
12-118376828-A-G	not specified	Uncertain significance (Apr 20, 2023)	2522670
12-118384051-G-T	not specified	Uncertain significance (Aug 10, 2023)	2617774
12-118386150-T-C	not specified	Uncertain significance (Apr 13, 2023)	2536781
12-118389928-A-T	not specified	Uncertain significance (Oct 25, 2023)	3171958
12-118391181-T-C	not specified	Uncertain significance (Jun 10, 2024)	3323528
12-118402002-C-T	not specified	Uncertain significance (May 13, 2024)	3323527
12-118403417-C-G	not specified	Uncertain significance (Apr 18, 2023)	2537561
12-118403496-A-G	not specified	Uncertain significance (Jul 17, 2023)	2590555
12-118411153-A-G	not specified	Uncertain significance (Jul 14, 2024)	3451115
12-118414397-C-T		Benign/Likely benign (Apr 01, 2023)	791587

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUDS3	protein_coding	protein_coding	ENST00000543473	12	41656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00454	0.994	124627	0	11	124638	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	96	167	0.576	0.00000867	2129
Missense in Polyphen		21	50.448	0.41627		644
Synonymous	1.22	49	61.1	0.801	0.00000313	572
Loss of Function	2.82	8	22.4	0.357	0.00000113	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000706	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000446	0.0000442
Middle Eastern	0.0000559	0.0000556
South Asian	0.000113	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Regulatory protein which represses transcription and augments histone deacetylase activity of HDAC1. May have a potential role in tumor suppressor pathways through regulation of apoptosis. May function in the assembly and/or enzymatic activity of the mSin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes. {ECO:0000269|PubMed:12724404, ECO:0000269|PubMed:21239494}.;
Pathway: NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Post-translational protein modification;HDACs deacetylate histones;Metabolism of proteins;Chromatin modifying enzymes;Ub-specific processing proteases;Deubiquitination;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.109

Intolerance Scores

loftool: 0.572
rvis_EVS: -0.23
rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

pHI: 0.210
hipred: Y
hipred_score: 0.506
ghis: 0.657

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.870

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Suds3
Phenotype: cellular phenotype; neoplasm; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Zebrafish Information Network

Gene name: suds3
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;apoptotic process;histone deacetylation;substantia nigra development;positive regulation of apoptotic process;negative regulation of transcription, DNA-templated
Cellular component: nucleus;nucleoplasm;cytosol;Sin3 complex;nuclear body;Sin3-type complex
Molecular function: histone deacetylase activity;protein binding;enzyme binding;histone deacetylase binding