Menu
GeneBe

LIN54

lin-54 DREAM MuvB core complex component

Basic information

Region (hg38): 4:82909972-83012926

Links

ENSG00000189308NCBI:132660OMIM:613367HGNC:25397Uniprot:Q6MZP7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LIN54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIN54 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
1
clinvar
1
missense
22
clinvar
22
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 22 1 0

Variants in LIN54

This is a list of pathogenic ClinVar variants found in the LIN54 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
4-82916975-T-C not specified Uncertain significance (Jun 10, 2024)3325851
4-82916982-G-A not specified Uncertain significance (Jul 05, 2022)2299707
4-82917014-G-C not specified Uncertain significance (Aug 09, 2021)2241948
4-82917018-A-G not specified Uncertain significance (Aug 22, 2023)2620988
4-82917027-A-G not specified Uncertain significance (Jul 06, 2022)2390363
4-82917030-T-G not specified Uncertain significance (Jun 18, 2021)2232967
4-82917035-C-G not specified Uncertain significance (Dec 21, 2023)3176940
4-82917180-T-C not specified Uncertain significance (Mar 15, 2024)3325844
4-82917186-T-C not specified Uncertain significance (Jun 21, 2021)2209234
4-82917201-T-G not specified Uncertain significance (Dec 22, 2023)3176941
4-82917233-T-C not specified Uncertain significance (Mar 15, 2024)3325845
4-82917284-A-G not specified Uncertain significance (Sep 27, 2022)2313855
4-82917320-G-T not specified Uncertain significance (Jun 04, 2024)3325843
4-82917327-C-T not specified Uncertain significance (Jan 16, 2024)3176933
4-82917349-T-A not specified Uncertain significance (May 07, 2024)3325850
4-82917365-G-A not specified Uncertain significance (Jun 07, 2024)3325840
4-82917375-T-C not specified Uncertain significance (Feb 17, 2023)2486815
4-82917381-T-C not specified Uncertain significance (Feb 15, 2023)2463289
4-82917394-C-A not specified Uncertain significance (Feb 13, 2024)3176934
4-82917410-C-G not specified Uncertain significance (Mar 07, 2024)3176935
4-82917455-T-C not specified Uncertain significance (Dec 14, 2021)2266845
4-82917668-G-A not specified Uncertain significance (Aug 16, 2022)2229056
4-82917710-C-T not specified Uncertain significance (May 24, 2023)2523124
4-82917734-A-G not specified Uncertain significance (Nov 18, 2022)2327320
4-82917747-G-A not specified Uncertain significance (Oct 12, 2022)2394961

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LIN54protein_codingprotein_codingENST00000340417 12102954
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.0000570124421051244260.0000201
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.702433940.6170.00001984809
Missense in Polyphen53111.650.474681377
Synonymous0.3971361420.9580.000007351557
Loss of Function5.29236.50.05480.00000206425

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00004680.0000443
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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}.;
Pathway
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;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec
0.0911

Intolerance Scores

loftool
0.00634
rvis_EVS
-0.54
rvis_percentile_EVS
20.54

Haploinsufficiency Scores

pHI
0.154
hipred
Y
hipred_score
0.783
ghis
0.557

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.903

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lin54
Phenotype

Gene ontology

Biological process
regulation of transcription, DNA-templated;cell cycle;regulation of cell cycle
Cellular component
nucleus;nucleoplasm
Molecular function
RNA polymerase II regulatory region sequence-specific DNA binding;DNA binding;protein binding;metal ion binding