SUPT3H

SPT3 homolog, SAGA and STAGA complex component, the group of MicroRNA protein coding host genes|SAGA complex

Basic information

Region (hg38): 6:44809316-45377953

Links

ENSG00000196284 ∙ NCBI:8464 ∙ OMIM:602947 ∙ HGNC:11466 ∙ Uniprot:O75486 ∙ 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 SUPT3H gene.

• Inborn genetic diseases (22 variants)
• not provided (10 variants)
• Cleidocranial dysostosis (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUPT3H 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						0
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1		5	6	4	16
Total	1	0	25	7	4

Variants in SUPT3H

This is a list of pathogenic ClinVar variants found in the SUPT3H region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44829851-A-G		not specified	Uncertain significance (Jul 20, 2021)
6-44932715-A-G		not specified	Uncertain significance (Feb 28, 2023)
6-44932731-G-C		not specified	Uncertain significance (Dec 01, 2022)
6-44953339-T-C		not specified	Uncertain significance (Dec 14, 2021)
6-44954539-C-T		not specified	Uncertain significance (Dec 21, 2022)
6-44961826-T-G		not specified	Uncertain significance (Oct 10, 2023)
6-45003673-C-G		not specified	Uncertain significance (Dec 19, 2022)
6-45003709-G-T		not specified	Uncertain significance (Sep 17, 2021)
6-45003751-T-A		not specified	Uncertain significance (Jun 29, 2023)
6-45003781-C-T		not specified	Uncertain significance (Jun 02, 2023)
6-45014815-T-C		not specified	Uncertain significance (Jun 21, 2021)
6-45014822-C-T		not specified	Uncertain significance (Jul 14, 2022)
6-45014830-T-C		not specified	Uncertain significance (Sep 06, 2022)
6-45014851-T-A		not specified	Uncertain significance (Oct 26, 2021)
6-45020556-C-T		not specified	Uncertain significance (Jun 21, 2022)
6-45020557-G-A		not specified	Uncertain significance (Oct 16, 2023)
6-45020565-A-G		not specified	Uncertain significance (Nov 17, 2022)
6-45020596-C-T		not specified	Uncertain significance (Dec 02, 2022)
6-45105960-A-C		not specified	Uncertain significance (Nov 21, 2022)
6-45105977-A-C		not specified	Uncertain significance (Oct 06, 2021)
6-45321795-C-A			Likely benign (Nov 15, 2018)
6-45321797-T-C		not specified	Uncertain significance (Feb 28, 2024)
6-45321826-T-C		not specified	Likely benign (Aug 14, 2023)
6-45321878-T-C		not specified	Uncertain significance (Jan 26, 2022)
6-45322901-T-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUPT3H	protein_coding	protein_coding	ENST00000371460	11	568637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.24e-11	0.162	125413	1	334	125748	0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.115	169	173	0.976	0.00000889	2175
Missense in Polyphen		44	51.455	0.85512		622
Synonymous	0.373	54	57.6	0.938	0.00000301	589
Loss of Function	0.647	18	21.2	0.849	0.00000123	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00307	0.00306
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.000164	0.000163
Finnish	0.00120	0.00120
European (Non-Finnish)	0.00131	0.00127
Middle Eastern	0.000164	0.000163
South Asian	0.00163	0.00157
Other	0.00236	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcriptional activator. {ECO:0000269|PubMed:9787080}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization;C-MYC pathway;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.909
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.14

Haploinsufficiency Scores

• pHI: 0.467
• hipred: Y
• hipred_score: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0618

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Supt3
• 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)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;histone deubiquitination;histone H3 acetylation;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;transcription factor TFIID complex;STAGA complex;transcription factor TFTC complex
• Molecular function: DNA binding;transcription coregulator activity;transcription coactivator activity;histone acetyltransferase activity;protein heterodimerization activity