LIX1L

limb and CNS expressed 1 like

Basic information

Region (hg38): 1:145933423-145958017

Links

ENSG00000271601 ∙ NCBI:128077 ∙ ∙ HGNC:28715 ∙ Uniprot:Q8IVB5 ∙ 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 LIX1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIX1L 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			21	1		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	21	1	0

Variants in LIX1L

This is a list of pathogenic ClinVar variants found in the LIX1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145936404-A-C		not specified	Uncertain significance (Aug 17, 2022)
1-145936423-C-G		not specified	Uncertain significance (Dec 02, 2022)
1-145936461-G-A		not specified	Uncertain significance (Mar 31, 2022)
1-145936468-T-G		not specified	Uncertain significance (Dec 13, 2023)
1-145937627-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-145937685-T-A		not specified	Uncertain significance (Apr 22, 2022)
1-145942735-G-C		not specified	Uncertain significance (Mar 22, 2023)
1-145942762-G-T		not specified	Uncertain significance (Feb 22, 2023)
1-145947641-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-145947662-C-G		not specified	Uncertain significance (Dec 11, 2023)
1-145947671-G-A		not specified	Uncertain significance (Aug 10, 2023)
1-145947686-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-145947757-T-G		not specified	Uncertain significance (Dec 15, 2022)
1-145957650-T-C		not specified	Uncertain significance (Sep 15, 2021)
1-145957668-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-145957695-C-G		not specified	Uncertain significance (Dec 27, 2022)
1-145957723-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-145957774-G-T		not specified	Uncertain significance (Jan 10, 2022)
1-145957800-G-T		not specified	Uncertain significance (Jun 18, 2021)
1-145957813-G-C		not specified	Uncertain significance (May 12, 2024)
1-145957825-T-C		not specified	Likely benign (Jan 23, 2023)
1-145957830-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-145957878-C-T		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.405
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.441
• hipred: Y
• hipred_score: 0.685

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lix1l

Zebrafish Information Network

• Gene name: lix1l
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: autophagy;biological_process;autophagosome maturation
• Cellular component: cellular_component;cytoplasm
• Molecular function: molecular_function