SUPT7L
protein-codingSPT7 like, STAGA complex subunit gamma, the group of SAGA complex
Gene summary
SUPT7L is a protein subunit of the human STAGA complex (SPT3; (MIM 602947)/TAF9 (MIM 600822)/GCN5 (MIM 602301) acetyltransferase complex), which is a chromatin-modifying multiprotein complex (Martinez et al., 2001 [PubMed 11564863]).[supplied by OMIM, Apr 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0006573
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0006573
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SUPT7L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014860.3. 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 | 2 | 2 | ||||
| missense | 1 | 63 | 64 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 2 | 0 | 66 | 0 | 0 | 68 |
Highest pathogenic variant AF is 0.000015733036
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055675.1 | 5 | MANE Select | |
| Ensembl | ENSP00000336750.5 | 5 | MANE Select | |
| RefSeq | NP_001269658.1 | 5 | Standard | |
| RefSeq | NP_001269659.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Chromatin modifying enzymes
- HATs acetylate histones
- Chromatin organization
- C-MYC pathway
- Validated targets of C-MYC transcriptional activation
Biological Process
- histone H3 acetylation
- maintenance of protein location in nucleus
- positive regulation of nucleic acid-templated transcription
Molecular Function
- transcription coactivator activity
- histone acetyltransferase activity
- protein binding
- protein heterodimerization activity
Cellular Component
- nucleus
- nucleoplasm
- STAGA complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000337768
- Coding exons
- 5
- Length
- 12998
- Individuals with no LoFs
- 124771
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 124804
- p
- 0.000132
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.943 | 200 | 241 | 0.829 | 0.0000134 | 2739 |
| Missense (PolyPhen) | 49 | 62.725 | 0.78119 | 644 | ||
| Synonymous | 0.525 | 80 | 86.2 | 0.928 | 0.00000447 | 814 |
| Loss of Function | 2.50 | 5 | 15.7 | 0.319 | 7.51e-7 | 186 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00026 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00021 | 0.00020 | rare |
| East Asian | 0.00017 | 0.00017 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0.00017 | 0.00016 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.288
Intolerance Scores
- RVIS EVS
- -0.14
- RVIS percentile EVS
- 43.57
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.956
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |