LLGL2

LLGL scribble cell polarity complex component 2, the group of Scribble complex|WD repeat domain containing

Basic information

Region (hg38): 17:75525080-75575209

Links

ENSG00000073350 ∙ NCBI:3993 ∙ OMIM:618483 ∙ HGNC:6629 ∙ Uniprot:Q6P1M3 ∙ 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 LLGL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LLGL2 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	3	4
missense			97	7	4	108
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	97	8	7

Variants in LLGL2

This is a list of pathogenic ClinVar variants found in the LLGL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75543431-G-C		not specified	Uncertain significance (May 24, 2023)
17-75543432-G-T		not specified	Uncertain significance (May 24, 2023)
17-75543463-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-75543478-C-T		not specified	Uncertain significance (Oct 03, 2022)
17-75543479-G-A		not specified	Uncertain significance (Apr 04, 2024)
17-75556068-A-G		not specified	Uncertain significance (May 18, 2022)
17-75556083-T-C		not specified	Uncertain significance (Jun 11, 2021)
17-75556091-A-G		not specified	Uncertain significance (Mar 01, 2023)
17-75556095-C-T		not specified	Uncertain significance (Mar 29, 2022)
17-75556103-C-T		not specified	Uncertain significance (Nov 28, 2023)
17-75556124-C-T		not specified	Uncertain significance (Dec 07, 2024)
17-75556125-G-A		not specified	Uncertain significance (Dec 15, 2023)
17-75558169-G-T		not specified	Uncertain significance (Mar 16, 2022)
17-75558199-A-G		not specified	Uncertain significance (Jan 10, 2023)
17-75558207-G-A		not specified	Uncertain significance (Mar 20, 2024)
17-75558211-C-A		not specified	Uncertain significance (Nov 15, 2024)
17-75558525-C-T		not specified	Uncertain significance (Jan 29, 2024)
17-75558566-G-T		not specified	Uncertain significance (Dec 15, 2023)
17-75558575-G-A		not specified	Uncertain significance (Jun 12, 2023)
17-75558582-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-75559323-C-T		not specified	Uncertain significance (Feb 27, 2024)
17-75559325-G-A		not specified	Uncertain significance (Oct 30, 2023)
17-75559337-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-75559355-C-A		not specified	Uncertain significance (Jun 18, 2024)
17-75559379-C-T		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LLGL2	protein_coding	protein_coding	ENST00000392550	25	50129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.88e-12	1.00	125673	0	70	125743	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.684	641	692	0.927	0.0000492	6513
Missense in Polyphen		228	256.3	0.88959		2489
Synonymous	0.0621	294	295	0.995	0.0000213	2124
Loss of Function	3.27	28	54.0	0.519	0.00000263	568

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000808	0.000782
Ashkenazi Jewish	0.000405	0.000397
East Asian	0.000171	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000345	0.000316
Middle Eastern	0.000171	0.000163
South Asian	0.000108	0.0000980
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of a complex with GPSM2/LGN, PRKCI/aPKC and PARD6B/Par-6, which may ensure the correct organization and orientation of bipolar spindles for normal cell division. This complex plays roles in the initial phase of the establishment of epithelial cell polarity. {ECO:0000269|PubMed:15632202}.
• Pathway: Tight junction - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.637
• rvis_EVS: 1.05
• rvis_percentile_EVS: 91.31

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.652
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.889

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Llgl2
• Phenotype: embryo 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); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: llgl2
• Affected structure: epidermal cell
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: exocytosis;regulation of Notch signaling pathway;cortical actin cytoskeleton organization;regulation of establishment or maintenance of cell polarity;positive regulation of GTPase activity;establishment of spindle orientation;cell division
• Cellular component: cytoplasm;cytosol;plasma membrane;cortical actin cytoskeleton;intracellular membrane-bounded organelle
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding;PDZ domain binding