SUPT5H
SPT5 homolog, DSIF elongation factor subunit
Basic information
Region (hg38): 19:39436156-39476670
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUPT5H 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 | 6 | |||||
| missense | 30 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | 2 | |||
| non coding | 3 | |||||
| Total | 0 | 0 | 31 | 3 | 6 |
Variants in SUPT5H
This is a list of pathogenic ClinVar variants found in the SUPT5H region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-39445959-G-C | not specified | Uncertain significance (Aug 02, 2022) | ||
| 19-39453392-AAAG-A | Benign (Jan 08, 2018) | |||
| 19-39453491-C-T | not specified | Uncertain significance (Jan 07, 2022) | ||
| 19-39458854-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 19-39459893-T-C | not specified | Uncertain significance (May 30, 2023) | ||
| 19-39459928-C-T | not specified | Uncertain significance (Jul 17, 2023) | ||
| 19-39459949-T-C | not specified | Uncertain significance (Sep 22, 2022) | ||
| 19-39459959-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
| 19-39464852-G-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 19-39464893-G-A | Benign (Oct 24, 2019) | |||
| 19-39465056-G-A | Likely benign (Nov 01, 2023) | |||
| 19-39466544-A-T | not specified | Uncertain significance (Sep 22, 2022) | ||
| 19-39466693-A-C | Benign (Dec 31, 2019) | |||
| 19-39466708-C-T | not specified | Uncertain significance (Mar 30, 2024) | ||
| 19-39468762-G-A | Likely benign (Feb 01, 2023) | |||
| 19-39469083-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 19-39469271-G-A | not specified | Uncertain significance (Nov 02, 2023) | ||
| 19-39469288-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 19-39469289-C-T | not specified | Uncertain significance (Jun 22, 2021) | ||
| 19-39469341-G-A | Uncertain significance (Feb 01, 2024) | |||
| 19-39469342-A-G | not specified | Uncertain significance (Apr 01, 2024) | ||
| 19-39470138-C-G | not specified | Uncertain significance (Dec 03, 2021) | ||
| 19-39470197-T-C | not specified | Uncertain significance (Dec 21, 2022) | ||
| 19-39470497-G-A | not specified | Uncertain significance (Jun 13, 2024) | ||
| 19-39471372-G-A | not specified | Uncertain significance (Dec 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SUPT5H | protein_coding | protein_coding | ENST00000599117 | 29 | 40515 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 3.15e-10 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.56 | 353 | 690 | 0.511 | 0.0000434 | 7138 |
| Missense in Polyphen | 77 | 200.45 | 0.38414 | 1873 | ||
| Synonymous | -0.264 | 274 | 268 | 1.02 | 0.0000174 | 2087 |
| Loss of Function | 7.32 | 1 | 64.5 | 0.0155 | 0.00000344 | 698 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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:10393184, ECO:0000269|PubMed:10421630, ECO:0000269|PubMed:10454543, ECO:0000269|PubMed:10757782, ECO:0000269|PubMed:10912001, ECO:0000269|PubMed:11112772, ECO:0000269|PubMed:11553615, ECO:0000269|PubMed:11809800, ECO:0000269|PubMed:12653964, ECO:0000269|PubMed:12718890, ECO:0000269|PubMed:14701750, ECO:0000269|PubMed:15136722, ECO:0000269|PubMed:15380072, ECO:0000269|PubMed:16214896, ECO:0000269|PubMed:9450929, ECO:0000269|PubMed:9514752, ECO:0000269|PubMed:9857195}.;
- Pathway
- Initiation of transcription and translation elongation at the HIV-1 LTR;mRNA Processing;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;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;RNA Pol II CTD phosphorylation and interaction with CE;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;RNA Polymerase II Transcription Elongation;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;mRNA Capping;Formation of the Early Elongation Complex
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- 0.00896
- rvis_EVS
- -1.42
- rvis_percentile_EVS
- 4.1
Haploinsufficiency Scores
- pHI
- 0.642
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.657
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Supt5
- Phenotype
- skeleton 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
- supt5h
- Affected structure
- hematopoietic multipotent progenitor cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;positive regulation of macroautophagy;negative regulation of DNA-templated transcription, elongation;positive regulation of DNA-templated transcription, elongation;positive regulation of transcription by RNA polymerase II;negative regulation of mRNA polyadenylation
- Cellular component
- nucleus;nucleoplasm;DSIF complex
- Molecular function
- chromatin binding;RNA binding;mRNA binding;protein binding;enzyme binding;protein heterodimerization activity