GeneBe

SUPT4H1

SPT4 homolog, DSIF elongation factor subunit

Basic information

Region (hg38): 17:58345175-58353093

Previous symbols: [ "SUPT4H" ]

Links

ENSG00000213246 ∙ NCBI:6827 ∙ OMIM:603555 ∙ HGNC:11467 ∙ Uniprot:P63272 ∙ 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 SUPT4H1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUPT4H1 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
4
clinvar
 4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 4 0 0

Variants in SUPT4H1

This is a list of pathogenic ClinVar variants found in the SUPT4H1 region.

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

Position Type Phenotype Significance ClinVar
17-58346292-C-A not specified Uncertain significance (Mar 21, 2023)2527913
17-58347217-G-A not specified Uncertain significance (Aug 26, 2022)2225309
17-58347231-C-A not specified Uncertain significance (Apr 04, 2023)2532406
17-58352110-T-C not specified Uncertain significance (Apr 25, 2023)2540103

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SUPT4H1protein_codingprotein_codingENST00000225504 57916
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0008770.8081257370111257480.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.254170.40.5820.00000380754
Missense in Polyphen1222.9530.52281269
Synonymous1.361827.00.6670.00000139225
Loss of Function1.1169.760.6156.50e-790

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.00004620.0000462
European (Non-Finnish)0.00005320.0000527
Middle Eastern0.0001090.000109
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites. DSIF can also positively regulate transcriptional elongation and is required for the efficient activation of transcriptional elongation by the HIV- 1 nuclear transcriptional activator, Tat. DSIF acts to suppress transcriptional pausing in transcripts derived from the HIV-1 LTR and blocks premature release of HIV-1 transcripts at terminator sequences. {ECO:0000269|PubMed:10075709, ECO:0000269|PubMed:10199401, ECO:0000269|PubMed:10454543, ECO:0000269|PubMed:10912001, ECO:0000269|PubMed:11112772, ECO:0000269|PubMed:11553615, ECO:0000269|PubMed:12653964, ECO:0000269|PubMed:12718890, ECO:0000269|PubMed:15136722, ECO:0000269|PubMed:15380072, ECO:0000269|PubMed:16214896, ECO:0000269|PubMed:9450929, ECO:0000269|PubMed:9857195}.;
Pathway
Initiation of transcription and translation elongation at the HIV-1 LTR;Disease;Formation of the HIV-1 Early Elongation Complex;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;Abortive elongation of HIV-1 transcript in the absence of Tat;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Elongation;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;Formation of the Early Elongation Complex (Consensus)

Recessive Scores

pRec
0.113

Intolerance Scores

loftool
0.448
rvis_EVS
0.21
rvis_percentile_EVS
67.72

Haploinsufficiency Scores

pHI
0.377
hipred
Y
hipred_score
0.807
ghis
0.547

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.982

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Supt4a
Phenotype
vision/eye phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;chromatin organization;chromatin remodeling;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;negative regulation of DNA-templated transcription, elongation;positive regulation of DNA-templated transcription, elongation;negative regulation of transcription elongation from RNA polymerase II promoter;positive regulation of transcription by RNA polymerase II
Cellular component
nucleus;nucleoplasm;DSIF complex
Molecular function
RNA polymerase II complex binding;DNA-binding transcription factor activity;single-stranded RNA binding;protein binding;zinc ion binding;protein heterodimerization activity