LLGL1

LLGL scribble cell polarity complex component 1, the group of WD repeat domain containing|Scribble complex

Basic information

Region (hg38): 17:18225635-18244875

Previous symbols: [ "DLG4", "LLGL", "HUGL", "HUGL-1" ]

Links

ENSG00000131899 ∙ NCBI:3996 ∙ OMIM:600966 ∙ HGNC:6628 ∙ Uniprot:Q15334 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LLGL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LLGL1 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				2	6	8
missense			61	3	3	67
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	61	5	9

Variants in LLGL1

This is a list of pathogenic ClinVar variants found in the LLGL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18225727-C-T			Likely benign (Nov 09, 2020)
17-18225762-A-G		not specified	Uncertain significance (Apr 08, 2023)
17-18229963-A-G			Benign (Oct 24, 2018)
17-18229974-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-18229990-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-18232497-A-G		not specified	Uncertain significance (Mar 28, 2024)
17-18232533-G-A		not specified	Uncertain significance (May 20, 2024)
17-18232571-G-A		not specified	Uncertain significance (Jan 03, 2022)
17-18232723-G-T		not specified	Uncertain significance (Sep 29, 2022)
17-18232785-C-T			Benign (May 30, 2018)
17-18233783-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-18233808-G-A			Benign (Jun 18, 2018)
17-18233827-A-A			Benign (Oct 10, 2018)
17-18233890-A-G		not specified	Uncertain significance (Apr 25, 2023)
17-18233920-G-T		not specified	Uncertain significance (Jul 19, 2022)
17-18233926-G-C		not specified	Uncertain significance (Apr 08, 2022)
17-18233933-G-A		not specified	Uncertain significance (Jun 23, 2021)
17-18234014-G-A			Benign (May 30, 2018)
17-18234023-G-A		not specified	Uncertain significance (May 25, 2022)
17-18234078-G-A		not specified	Likely benign (Apr 19, 2024)
17-18234147-G-A		not specified	Uncertain significance (Jul 25, 2023)
17-18234156-A-G		not specified	Likely benign (Jan 08, 2024)
17-18234310-C-G		not specified	Uncertain significance (Nov 18, 2023)
17-18234376-C-G		not specified	Uncertain significance (Sep 22, 2022)
17-18234687-C-T		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LLGL1	protein_coding	protein_coding	ENST00000316843	22	19289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000247	1.00	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	575	682	0.843	0.0000464	6823
Missense in Polyphen		188	267.13	0.70377		2671
Synonymous	-2.16	341	294	1.16	0.0000212	2261
Loss of Function	4.16	17	48.1	0.353	0.00000247	508

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000342	0.000334
Ashkenazi Jewish	0.000399	0.000397
East Asian	0.0000544	0.0000544
Finnish	0.000147	0.000139
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000987	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cortical cytoskeleton protein found in a complex involved in maintaining cell polarity and epithelial integrity. Involved in the regulation of mitotic spindle orientation, proliferation, differentiation and tissue organization of neuroepithelial cells. Involved in axonogenesis through RAB10 activation thereby regulating vesicular membrane trafficking toward the axonal plasma membrane. {ECO:0000269|PubMed:15735678, ECO:0000269|PubMed:16170365}.
• Pathway: Tight junction - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.326
• rvis_EVS: -1.74
• rvis_percentile_EVS: 2.43

Haploinsufficiency Scores

• pHI: 0.184
• hipred: Y
• hipred_score: 0.694
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.817

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Llgl1
• 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); 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); embryo phenotype; skeleton 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); craniofacial phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: llgl1
• Affected structure: peridermal cell
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: exocytosis;Golgi to plasma membrane transport;axonogenesis;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;protein-containing complex assembly
• Cellular component: Golgi cis cisterna;cytoplasm;cytoskeleton;plasma membrane;axon;cortical actin cytoskeleton;early endosome membrane;trans-Golgi network membrane
• Molecular function: GTPase activator activity;structural molecule activity;protein binding;Rab GTPase binding;protein kinase binding