LIN54
protein-codinglin-54 DREAM MuvB core complex component
Gene summary
LIN54 is a component of the LIN, or DREAM, complex, an essential regulator of cell cycle genes (Schmit et al., 2009 [PubMed 19725879]).[supplied by OMIM, Dec 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~103.0 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 LIN54 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_194282.4. 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 | 2 | 3 | |||
| missense | 59 | 59 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 61 | 2 | 0 | 63 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_919258.2 | 12 | MANE Select | |
| Ensembl | ENSP00000341947.3 | 12 | MANE Select | |
| RefSeq | NP_001108479.1 | 12 | Standard | |
| RefSeq | NP_001108480.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cellular senescence - Homo sapiens (human)
- Polo-like kinase mediated events
- Transcription of E2F targets under negative control by DREAM complex
- G0 and Early G1
- Mitotic G1-G1/S phases
Biological Process
- regulation of transcription, DNA-templated
- cell cycle
- regulation of cell cycle
Molecular Function
- RNA polymerase II regulatory region sequence-specific DNA binding
- DNA binding
- protein binding
- metal ion binding
Cellular Component
- nucleus
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000340417
- Coding exons
- 12
- Length
- 102954
- Individuals with no LoFs
- 124421
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 124426
- p
- 0.0000201
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.70 | 243 | 394 | 0.617 | 0.0000198 | 4809 |
| Missense (PolyPhen) | 53 | 111.65 | 0.47468 | 1377 | ||
| Synonymous | 0.397 | 136 | 142 | 0.958 | 0.00000735 | 1557 |
| Loss of Function | 5.29 | 2 | 36.5 | 0.0548 | 0.00000206 | 425 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000047 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the DREAM complex, a multiprotein complex that can both act as a transcription activator or repressor depending on the context (PubMed:17671431, PubMed:17531812). In G0 phase, the complex binds to more than 800 promoters and is required for repression of E2F target genes (PubMed:17671431, PubMed:17531812). In S phase, the complex selectively binds to the promoters of G2/M genes whose products are required for mitosis and participates in their cell cycle dependent activation (PubMed:17671431, PubMed:17531812). In the complex, acts as a DNA- binding protein that binds the promoter of CDK1 in a sequence- specific manner (PubMed:19725879). Specifically recognizes the consensus motif 5'-TTYRAA-3' in target DNA (PubMed:27465258). {ECO:0000269|PubMed:17531812, ECO:0000269|PubMed:17671431, ECO:0000269|PubMed:19725879, ECO:0000269|PubMed:27465258}.;
Recessive Scores
- pRec
- 0.0911
Intolerance Scores
- LoFtool
- 0.00634
- RVIS EVS
- -0.54
- RVIS percentile EVS
- 20.54
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |