GID4
protein-codingGID complex subunit 4 homolog
Gene summary
The multiprotein Mediator complex is a coactivator required for activation of RNA polymerase II transcription by DNA bound transcription factors. The protein encoded by this gene is thought to be a subunit of the Mediator complex. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]
- C17orf39
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.0 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 GID4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024052.5. 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 | 1 | 3 | |||
| missense | 28 | 28 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 30 | 1 | 0 | 31 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_076957.3 | 6 | MANE Select | |
| Ensembl | ENSP00000268719.4 | 6 | MANE Select | |
| RefSeq | NP_001397986.1 | 4 | Standard | |
| Ensembl | ENSP00000365523.3 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein ubiquitination
- proteasome-mediated ubiquitin-dependent protein catabolic process
Molecular Function
- ubiquitin protein ligase activity
Cellular Component
- ubiquitin ligase complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000268719
- Coding exons
- 6
- Length
- 29113
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125728
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.10 | 64 | 132 | 0.485 | 0.00000680 | 1904 |
| Missense (PolyPhen) | 14 | 46.13 | 0.30349 | 566 | ||
| Synonymous | 1.87 | 36 | 53.3 | 0.675 | 0.00000282 | 616 |
| Loss of Function | 3.02 | 1 | 12.5 | 0.0799 | 5.29e-7 | 164 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Substrate-recognition subunit of the CTLH E3 ubiquitin- protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 (Probable) (PubMed:29911972). Binds proteins and peptides with a Pro/N-degron consisting of an unmodified N-terminal Pro followed by a small residue, and has the highest affinity for the peptide Pro-Gly-Leu- Trp (PubMed:29632410). Binds peptides with an N-terminal sequence of the type Pro-[Ala,Gly]-[Leu,Met,Gln,Ser,Tyr]- [Glu,Gly,His,Ser,Val,Trp,Tyr]. Does not bind peptides with an acetylated N-terminal Pro residue (PubMed:29632410). {ECO:0000269|PubMed:29632410, ECO:0000269|PubMed:29911972, ECO:0000305}.;
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |