LIN52

lin-52 DREAM MuvB core complex component

Basic information

Region (hg38): 14:74084955-74201493

Previous symbols: [ "C14orf46" ]

Links

ENSG00000205659 ∙ NCBI:91750 ∙ ∙ HGNC:19856 ∙ Uniprot:Q52LA3 ∙ 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 LIN52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIN52 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in LIN52

This is a list of pathogenic ClinVar variants found in the LIN52 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-74091276-C-T		not specified	Uncertain significance (Nov 21, 2023)
14-74095960-C-T		not specified	Uncertain significance (Dec 19, 2022)
14-74095979-C-G		not specified	Uncertain significance (Apr 23, 2024)
14-74097813-C-G		not specified	Uncertain significance (Jun 18, 2021)
14-74097837-G-A		not specified	Uncertain significance (Aug 02, 2023)
14-74097848-G-A		not specified	Uncertain significance (Apr 13, 2022)
14-74101173-C-T		not specified	Uncertain significance (Nov 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIN52	protein_coding	protein_coding	ENST00000555028	6	116438

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.918	0.0812	125695	0	1	125696	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	39	62.4	0.625	0.00000328	752
Missense in Polyphen		6	13.766	0.43587		195
Synonymous	1.51	12	20.7	0.579	0.00000105	213
Loss of Function	2.63	0	8.04	0.00	4.07e-7	91

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)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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: 0.130

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.556
• hipred: Y
• hipred_score: 0.580
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lin52

Gene ontology

• Biological process: transcription, DNA-templated;regulation of cell cycle
• Cellular component: nucleoplasm;DRM complex