LIN54

lin-54 DREAM MuvB core complex component

Basic information

Region (hg38): 4:82909973-83012926

Links

ENSG00000189308 ∙ NCBI:132660 ∙ OMIM:613367 ∙ HGNC:25397 ∙ Uniprot:Q6MZP7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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		1
missense			22			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)
4-82916982-G-A		not specified	Uncertain significance (Jul 05, 2022)
4-82917014-G-C		not specified	Uncertain significance (Aug 09, 2021)
4-82917018-A-G		not specified	Uncertain significance (Aug 22, 2023)
4-82917027-A-G		not specified	Uncertain significance (Jul 06, 2022)
4-82917030-T-G		not specified	Uncertain significance (Jun 18, 2021)
4-82917035-C-G		not specified	Uncertain significance (Dec 21, 2023)
4-82917180-T-C		not specified	Uncertain significance (Mar 15, 2024)
4-82917186-T-C		not specified	Uncertain significance (Jun 21, 2021)
4-82917201-T-G		not specified	Uncertain significance (Dec 22, 2023)
4-82917233-T-C		not specified	Uncertain significance (Mar 15, 2024)
4-82917284-A-G		not specified	Uncertain significance (Sep 27, 2022)
4-82917320-G-T		not specified	Uncertain significance (Jun 04, 2024)
4-82917327-C-T		not specified	Uncertain significance (Jan 16, 2024)
4-82917349-T-A		not specified	Uncertain significance (May 07, 2024)
4-82917365-G-A		not specified	Uncertain significance (Jun 07, 2024)
4-82917375-T-C		not specified	Uncertain significance (Feb 17, 2023)
4-82917381-T-C		not specified	Uncertain significance (Feb 15, 2023)
4-82917394-C-A		not specified	Uncertain significance (Feb 13, 2024)
4-82917410-C-G		not specified	Uncertain significance (Mar 07, 2024)
4-82917455-T-C		not specified	Uncertain significance (Dec 14, 2021)
4-82917668-G-A		not specified	Uncertain significance (Aug 16, 2022)
4-82917710-C-T		not specified	Uncertain significance (May 24, 2023)
4-82917734-A-G		not specified	Uncertain significance (Nov 18, 2022)
4-82917747-G-A		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIN54	protein_coding	protein_coding	ENST00000340417	12	102954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000570	124421	0	5	124426	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	243	394	0.617	0.0000198	4809
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000468	0.0000443
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lin54

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