SUPT6H

SPT6 homolog, histone chaperone and transcription elongation factor, the group of SH2 domain containing

Basic information

Region (hg38): 17:28662197-28702679

Links

ENSG00000109111 ∙ NCBI:6830 ∙ OMIM:601333 ∙ HGNC:11470 ∙ Uniprot:Q7KZ85 ∙ 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 SUPT6H gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUPT6H 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				4		4
missense			59			59
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	59	5	0

Variants in SUPT6H

This is a list of pathogenic ClinVar variants found in the SUPT6H region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28673486-A-G		not specified	Uncertain significance (Mar 17, 2023)
17-28674291-G-A		not specified	Uncertain significance (Mar 30, 2024)
17-28674296-G-C		not specified	Uncertain significance (Feb 27, 2023)
17-28674423-C-T		not specified	Uncertain significance (Nov 02, 2023)
17-28674546-A-T		not specified	Uncertain significance (Mar 08, 2024)
17-28674982-C-T		not specified	Uncertain significance (Jul 12, 2023)
17-28675005-C-G		not specified	Uncertain significance (Jan 16, 2024)
17-28675012-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-28675129-C-T		not specified	Uncertain significance (Feb 14, 2023)
17-28675408-C-T			Likely benign (Jul 01, 2022)
17-28676318-G-A		not specified	Uncertain significance (Nov 17, 2022)
17-28676369-G-A		not specified	Uncertain significance (Oct 06, 2021)
17-28677779-A-G		not specified	Uncertain significance (Aug 17, 2021)
17-28678097-C-G		not specified	Uncertain significance (Jan 22, 2024)
17-28678142-A-G		not specified	Uncertain significance (Nov 08, 2022)
17-28678558-C-T		not specified	Uncertain significance (Oct 14, 2023)
17-28678600-A-G		not specified	Uncertain significance (Dec 16, 2023)
17-28678619-G-T		not specified	Uncertain significance (Jan 12, 2024)
17-28678621-A-T		not specified	Uncertain significance (Apr 13, 2022)
17-28681275-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-28681350-G-A		not specified	Uncertain significance (Apr 09, 2024)
17-28681908-G-C		not specified	Uncertain significance (May 02, 2024)
17-28681921-C-T		not specified	Uncertain significance (Oct 30, 2023)
17-28681935-G-T		not specified	Uncertain significance (Jun 11, 2021)
17-28682758-C-T			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUPT6H	protein_coding	protein_coding	ENST00000314616	36	40589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.78e-15	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.14	564	1.03e+3	0.549	0.0000614	11476
Missense in Polyphen		85	266.22	0.31929		2818
Synonymous	0.786	360	379	0.949	0.0000219	3150
Loss of Function	9.17	4	106	0.0378	0.00000628	1114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription elongation factor which binds histone H3 and plays a key role in the regulation of transcription elongation and mRNA processing. Enhances the transcription elongation by RNA polymerase II (RNAPII) and is also required for the efficient activation of transcriptional elongation by the HIV-1 nuclear transcriptional activator, Tat. Besides chaperoning histones in transcription, acts to transport and splice mRNA by forming a complex with IWS1 and the C-terminal domain (CTD) of the RNAPII subunit RPB1 (POLR2A). The SUPT6H:IWS1:CTD complex recruits mRNA export factors (ALYREF/THOC4, EXOSC10) as well as histone modifying enzymes (such as SETD2), to ensure proper mRNA splicing, efficient mRNA export and elongation-coupled H3K36 methylation, a signature chromatin mark of active transcription. SUPT6H via its association with SETD1A, regulates both class-switch recombination and somatic hypermutation through formation of H3K4me3 epigenetic marks on activation-induced cytidine deaminase (AICDA) target loci. Promotes the activation of the myogenic gene program by entailing erasure of the repressive H3K27me3 epigenetic mark through stabilization of the chromatin interaction of the H3K27 demethylase KDM6A. {ECO:0000269|PubMed:15060154, ECO:0000269|PubMed:17234882, ECO:0000269|PubMed:22316138, ECO:0000269|PubMed:23503590, ECO:0000269|PubMed:9514752}.
• Pathway: Gene expression (Transcription);RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;RNA Polymerase II Transcription Elongation (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.0216
• rvis_EVS: -2.41
• rvis_percentile_EVS: 1.07

Haploinsufficiency Scores

• pHI: 0.832
• hipred: Y
• hipred_score: 0.860
• ghis: 0.642

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Supt6
• 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: supt6h
• Affected structure: pigment cell
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: blastocyst formation;chromatin remodeling;regulation of transcription, DNA-templated;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;mRNA processing;RNA splicing;regulation of mRNA export from nucleus;viral process;positive regulation of transcription elongation from RNA polymerase II promoter;nucleosome organization;mRNA transcription by RNA polymerase II;regulation of isotype switching;regulation of mRNA processing;mRNA transport;regulation of muscle cell differentiation;negative regulation of histone H3-K27 methylation;chromatin maintenance
• Cellular component: nucleus;nucleoplasm;transcription elongation factor complex;transcriptionally active chromatin
• Molecular function: DNA binding;DNA-binding transcription factor activity;RNA binding;protein binding;nucleosome binding;histone binding