SUPT20H
protein-codingSPT20 homolog, SAGA complex component, the group of SAGA complex
Gene summary
Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Part of SAGA-type complex. [provided by Alliance of Genome Resources, Jun 2026]
- C13orf19
- FAM48A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SUPT20H variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001014286.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 91 | 1 | 92 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 99 | 2 | 0 | 101 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001014308.2 | 25 | MANE Select | |
| Ensembl | ENSP00000218894.10 | 25 | MANE Select | |
| RefSeq | NP_001265409.1 | 24 | Standard | |
| RefSeq | NP_001265410.1 | 24 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Autophagy - animal - Homo sapiens (human)
- Chromatin modifying enzymes
- HATs acetylate histones
- Chromatin organization
Biological Process
- regulation of transcription by RNA polymerase II
- autophagy
- gastrulation
- positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter
Molecular Function
- transcription coregulator activity
- protein binding
Cellular Component
- SAGA complex
- fibrillar center
- SAGA-type complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000350612
- Coding exons
- 25
- Length
- 50402
- Individuals with no LoFs
- 125690
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 58
- Defined
- 125748
- p
- 0.000231
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 325 | 391 | 0.832 | 0.0000193 | 5031 |
| Missense (PolyPhen) | 53 | 75.86 | 0.69865 | 1021 | ||
| Synonymous | 0.651 | 126 | 136 | 0.929 | 0.00000676 | 1479 |
| Loss of Function | 2.66 | 30 | 50.3 | 0.596 | 0.00000236 | 631 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.00020 | 0.00016 | rare |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down- regulation of E-cadherin during gastrulation by regulating E- cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by FGF signaling and Snail (By similarity). Required for starvation- induced ATG9A trafficking during autophagy. {ECO:0000250, ECO:0000269|PubMed:19893488}.;
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- RVIS EVS
- -0.44
- RVIS percentile EVS
- 24.46
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- K
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |