LIN9

lin-9 DREAM MuvB core complex component

Basic information

Region (hg38): 1:226231149-226309869

Links

ENSG00000183814 ∙ NCBI:286826 ∙ OMIM:609375 ∙ HGNC:30830 ∙ Uniprot:Q5TKA1 ∙ 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 LIN9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIN9 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			1			1
Total	0	0	23	0	1

Variants in LIN9

This is a list of pathogenic ClinVar variants found in the LIN9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-226233123-T-C		not specified	Uncertain significance (Aug 02, 2021)
1-226233476-C-T		not specified	Uncertain significance (Sep 14, 2022)
1-226233487-G-C		not specified	Uncertain significance (Nov 30, 2022)
1-226233494-T-C			Benign (Nov 09, 2018)
1-226238979-A-G		not specified	Uncertain significance (Feb 05, 2024)
1-226239059-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-226265606-G-A		not specified	Uncertain significance (Apr 04, 2023)
1-226266235-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-226266236-G-T		not specified	Uncertain significance (Mar 14, 2023)
1-226266247-A-G		not specified	Uncertain significance (Jul 11, 2023)
1-226266250-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-226266259-G-A		not specified	Uncertain significance (May 03, 2023)
1-226266281-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-226267977-T-C		not specified	Uncertain significance (Oct 13, 2023)
1-226277786-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-226277829-T-C		not specified	Uncertain significance (Jul 26, 2022)
1-226286403-T-C		not specified	Uncertain significance (Dec 04, 2023)
1-226287782-T-C		not specified	Uncertain significance (Mar 14, 2023)
1-226295853-T-C		not specified	Uncertain significance (Dec 15, 2022)
1-226295910-C-G		not specified	Uncertain significance (Jun 16, 2023)
1-226297748-C-A		not specified	Uncertain significance (Aug 01, 2022)
1-226297757-C-T		not specified	Uncertain significance (Jun 01, 2023)
1-226309123-T-C		not specified	Uncertain significance (Dec 06, 2022)
1-226309130-G-A		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIN9	protein_coding	protein_coding	ENST00000328205	15	78721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00229	125735	0	3	125738	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	176	291	0.605	0.0000151	3659
Missense in Polyphen		29	87.448	0.33163		1068
Synonymous	0.462	93	98.8	0.941	0.00000490	1030
Loss of Function	4.89	4	35.4	0.113	0.00000198	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000295	0.0000295
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000896	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a tumor suppressor. Inhibits DNA synthesis. Its ability to inhibit oncogenic transformation is mediated through its association with RB1. Plays a role in the expression of genes required for the G1/S transition. {ECO:0000269|PubMed:15538385, ECO:0000269|PubMed:16730350}.
• Pathway: Cellular senescence - Homo sapiens (human);Gastric Cancer Network 1;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: 0.421

Intolerance Scores

• loftool: 0.102
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.534
• hipred: Y
• hipred_score: 0.783
• ghis: 0.576

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.239

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lin9
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; embryo phenotype; immune system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: lin9
• Affected structure: olfactory system
• Phenotype tag: abnormal
• Phenotype quality: apoptotic

Gene ontology

• Biological process: reproduction;transcription, DNA-templated;cell cycle;regulation of cell cycle;DNA biosynthetic process
• Cellular component: nucleoplasm;transcriptional repressor complex
• Molecular function: DNA binding;protein binding